Alignment and Data Format

Total Page:16

File Type:pdf, Size:1020Kb

Alignment and Data Format High-throughput Sequencing and Translational Genomics Alignment and Data Format Elena Piñeiro-Yáñez ([email protected]) CNIO BIOINFORMATICS UNIT Alignments What is an alignment? ACGTCTTGACTGG -TTAAAATAC AC - TCTTGACTGGATTAACATAC Sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Elements ACGTTTTGCAGTAAATGCGGACTGA - T ACGTTGTGCAGTAAATGCGGA -- GACT mismatch match gap (insertion/deletion) Alignment seeks to reduce gaps and mismatches and maximize matches. In the construction, each of these components has a penalty value associated. For gaps there is a penalty value for opening the gap and another for extending it. ACGTTTTGCAGTAAATGCGGACTGAT ACGTTTTGCAGTAAATGCGGACTGAT ACGTTTTGCAGTAAATGCGGACTGA -T ACGTTGTGCAGTAAATGCGGA-GACT ACGTTGTGCAGTAAATGCGGA -- GACT ACGTTGTGCAGTAAATGCGGA --GACT 1 gap 1 extended gap 2 gaps Types 1. Based on the number of sequences: • Pairwise alignment: 2 sequences • Multiple alignment: > 2 sequences 2. Based on the region to align: • Local: sequence sub-region (Smith and Waterman, BLAST) Alignment is done only in the most similar regions • Global: complete sequence (Needleman Wunsch) Alignment covers two sequences completely To align sequences that start and end in the same region (homologous genes of similar species) Objectives The comparison between sequences in sequence alignment allows to: 1. Determine the homology degree 2. Identify functional domains 3. Compare the gene with its product 4. Find homologous positions 5. Identify differences Objectives The comparison between sequences in sequence alignment allows to: 1. Determine the homology degree 2. Identify functional domains 3. Compare the gene with its product 4. Find homologous positions 5. Identify differences Differential Expression and Variant Detection in Next Generation Sequencing (NGS) NGS https://www.youtube.com/watch?v=fCd6B5HRaZ8 One of the earliest and important steps in NGS analysis is the mapping of the reads to the original reference. This is the Read Alignment Classical vs NGS alignment Classical NGS Quantity A few sequences (n < 30) between them Billions of reads to a very large reference genome (n = 106 - 108 ) Length Long sequences (a whole gene, including introns, or a whole protein) Reads have short sequences (I = 25-1000 bp) Similarity No very similar sequences Highly similar sequences Quality High quality sequences coming from Sanger capillary sequencing Lower quality sequences Examples ClustalW, T-Coffee BWA, Bowtie Short Read Aligners Challenges • As we need to align billions of reads to a very large reference genome -> SRA must be "extraordinarily efficient algorithms": • Speed • Memory use • As we need to align short reads, a read may align in multiple positions -> SRA have to: • Either report multiple positions • Or pick heuristically one of them • Different NGS technologies have different error profiles to take into account: • 454: insertion or deletions in homopolymer runs • Illumina: increasing likelihood of sequence errors towards the end of the read • Specific problems: splicing junctions in RNAseq Timeline From https://www.ebi.ac.uk/~nf/hts_mappers/ DNA mappers are plotted in blue RNA mappers in red miRNA mappers in green bisulfite mappers in purple Gray dotted lines connect related mappers (extensions or new major versions). The time line only includes mappers with peer- reviewed publications and the date corresponds to the earliest date of publication Elements to consider in the alignment • Read type (DNA, RNA, ...) Read type InRNAseq the problem is the splicing RNAseq aligners have to allow long gaps in the alignment for those reads that span splice junctions Nature Biotechnology 28, 421–423(2010) Elements to consider in the alignment • Read type (DNA, RNA, ...) • Read length: • extremely short sequences (miRNA) • Increasing length of the reads (more probability of mismatches and gaps) Elements to consider in the alignment • Read type (DNA, RNA, ...) • Read length: • extremely short sequences (miRNA) • Increasing length of the reads (more probability of mismatches and gaps) • Paired-end or single-end Pair-end reads https://www.illumina.com/science/technology/next-generation-sequencing/paired-end-vs-single-read-sequencing.html Elements to consider in the alignment • Read type (DNA, RNA, ...) • Read length: • extremely short sequences (miRNA) • Increasing length of the reads (more probability of mismatches and gaps) • Paired-end or not • Computational requirements (number of processors, memory) • Base quality (taken or not into account) • Sequencing errors (can be platform dependent) • Number of mismatches (limitation in allowed differences) Reference Genome Human Reference Genome Equivalent UCSC Release name Date of release Base Pairs version GRCh38 Dec 2013 hg38 3,609,003,417 GRCh37 Feb 2009 hg19 3,326,743,047 REFERENCE GENOME Reads Problem with dimension of data Indexing Indexing allows to organize information in a more easier and faster way to search Spaced seeds vs Burrows-Wheeler Spaced seeds Slower More mismatches allowed Indel detection Unspliced: MAQ, GSNAP Spliced: GMAP Burrows-Wheeler Transform (BWT) Faster Few mismatches allowed Limited indel detection Unspliced: BWA, Bowtie Spliced: TopHat Due to the increase in the quality of the reads and the increase in depth and coverage, BWT aligners are more common Nat Biotechnol. 2009 May; 27(5): 455–457 Errors and biases • Errors in reference sequence • Sequencing errors: • Increases mismatches • Higher at the end of the reads • Different regions in DNA sequence causes aligning biases: • Repetitive regions: • Similar regions in different locations • Place of sequencing errors • Place of real mutations and structural variants • Difficulties in the alignment of insertions/deletions (gaps) Solutions: Quality Control Post-alignment, mapping quality scores, local realignment of indels Data formats Data formats Sequencing Reads FASTQ/FAST5/ HDF5 Reference Genome Alignment FASTA Alignments Reference Intervals SAM/BAM/CRAM Transcriptome BED GTF/GFF Variant Calling RNAseq Variants Counts VCF TSV/CSV Reference Genome – FASTA format • Typical extensions: .fasta, .fas, .fa, .fna, .fsa • Each sequence is composed by at least two consecutive lines: • ">" Sequence name and optional description (space separated) • Line(s) with the whole sequence We can have multiple sequences in the same file (multifasta) Reference Genome – FASTA format IUPAC nucleotide code Base A Adenine C Cytosine G Guanine T (or U) Thymine (or Uracil) R A or G Y C or T Nucleotide codes S G or C (IUPAC) W A or T K G or T M A or C B C or G or T D A or G or T H A or C or T V A or C or G N any base . or - gap Reads - FASTQ • Typical extensions: .fq, .fastq • Each read is composed by 4 lines: • "@" Read name and optional description (space separated) • Sequence • "+" (optionally: repeat the read name) • Base Quality Score Reads – FASTQ – Quality Score • Phred quality scores QPhred are defined as a property which is logarithmically related to the base- calling error probabilities p QPhred = -10 log10(p) • The score is written as the character whose ASCII code is QPhred + 33 • The higher the the QPhred , the lower the probability that the base calling is erroneous Reads – FASTQ – ASCII code Reads – FASTQ – Single-end/Paired-end One unique sample can have 1 or 2 files: • If single-end Seq -> 1 file (name ".fastq") • If paired-end Seq -> 2 files (names "_R1.fastq" "_R2.fastq") Alignment - SAM/BAM • SAM is the human readable text format (.sam extension) • BAM is the binary, machine efficient format (.bam extension) • Both contains exactly the same information and are interconvertible (samtools) File specifications: https://samtools.github.io/hts-specs/SAMv1.pdf Alignment - SAM/BAM - Header Alignment - SAM/BAM - Alignments If single-end: 7. reference sequence name of the alignment of the next read in sequence 8. position in the alignment of the next read in sequence 9. number of bases covered by reads from the same fragment. Plus/minus means the current read is the leftmost/rightmost read SAM FLAGS Alignment - SAM/BAM - CIGAR • Concise Idiosyncratic Gapped Alignment Report • It is a compressed representation of an alignment • Format: A CIGAR string is made up of <integer><op> pairs • Here, "op" is an operation specified as a single character, usually an upper-case letter (see table) Alignment - CRAM • Typical extension: .cram • CRAM files are alignment files like BAM files • They represent a compressed version of the alignment. This compression is driven by the reference the sequence data is aligne d to • The file format was designed by the EBI to reduce the disk footprint of alignment data in these days of ever-increasing data volumes • Full compatibility with BAM • Effortless transition to CRAM from using BAM files • Now is not very often used, but it probably will be the alignment format for the next few years • Cramtools Intervals - BED • Typical extension: .bed • The first three are required BED fields, the rest are optional 1. chrom - The name of the chromosome (e.g. chr3, chrY, chr2) 2. chromStart - The starting position of the feature in the chromosome. 0-based (The first base in a chromosome is numbered 0) 3. chromEnd - The ending position of the feature in the chromosome or scaffold • Additionally, 9 optional fields: 4. name - Defines the name of the BED line. 5. Score (. or a number between 0 and 1000). 6. strand (+ forward, - reverse)
Recommended publications
  • Sequence Alignment/Map) Is a Text Format for Storing Sequence Alignment Data in a Series of Tab Delimited ASCII Columns
    NGS FILE FORMATS SEQUENCE FILE FORMATS FASTA FORMAT FASTA Single sequence example: >HWI-ST398_0092:1:1:5372:2486#0/1 TTTTTCGTTCTTTTCATGTACCGCTTTTTGTTCGGTTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAT ACGTAGCAGCAGCATCAGTACGACTACGACGACTAGCACATGCGACGATCGATGCTAGCTGACTATCGATG Multiple sequence example: >Sequence Name 1 TTTTTCGTTCTTTTCATGTACCGCTTTTTGTTCGGTTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAT ACGTAGCAGCAGCATCAGTACGACTACGACGACTAGCACATGCGACGATCGATGCTAGCTGACTATCGATG >Sequence Name 2 ACGTAGACACGACTAGCATCAGCTACGCATCGATCAGCATCGACTAGCATCACACATCGATCAGCATCACGACTAGCAT AGCATCGACTACACTACGACTACGATCCACGTACGACTAGCATGCTAGCGCTAGCTAGCTAGCTAGTCGATCGATGAGT AGCTAGCTAGCTAGC >Sequence Name 3 ACTCAGCATGCATCAGCATCGACTACGACTACGACATCGACTAGCATCAGCAT SEQUENCE FILE FORMATS FASTQ FORMAT FASTQ Text based format for storing sequence data and corresponding quality scores for each base. To enable a one-one correspondence between the base sequence and the quality score the score is stored as a single one letter/number code using an offset of the standard ASCII code. Quality scores range from 0 to 40 and represent a log10 score for the probability of being wrong. E.g. score of 30 => 1:1000 chance of error SEQUENCE FILE FORMATS FASTQ FORMAT FASTQ Each fastq file contain multiple entries and each entry consists of 4 lines: 1. header line beginning with “@“ and sequence name 2. sequence line 3. header line beginning with “+” which can have the name but rarely does 4. quality score line SEQUENCE FILE FORMATS FASTQ FORMAT FASTQ @HWI-ST398_0092:6:73:5372:2486#0/1 TTTTTCGTTCTTTTCATGTACCGCTTTTTGTTCGGTTAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGAT
    [Show full text]
  • Alternate-Locus Aware Variant Calling in Whole Genome Sequencing Marten Jäger1,2, Max Schubach1, Tomasz Zemojtel1,Knutreinert3, Deanna M
    Jäger et al. Genome Medicine (2016) 8:130 DOI 10.1186/s13073-016-0383-z RESEARCH Open Access Alternate-locus aware variant calling in whole genome sequencing Marten Jäger1,2, Max Schubach1, Tomasz Zemojtel1,KnutReinert3, Deanna M. Church4 and Peter N. Robinson1,2,3,5,6* Abstract Background: The last two human genome assemblies have extended the previous linear golden-path paradigm of the human genome to a graph-like model to better represent regions with a high degree of structural variability. The new model offers opportunities to improve the technical validity of variant calling in whole-genome sequencing (WGS). Methods: We developed an algorithm that analyzes the patterns of variant calls in the 178 structurally variable regions of the GRCh38 genome assembly, and infers whether a given sample is most likely to contain sequences from the primary assembly, an alternate locus, or their heterozygous combination at each of these 178 regions. We investigate 121 in-house WGS datasets that have been aligned to the GRCh37 and GRCh38 assemblies. Results: We show that stretches of sequences that are largely but not entirely identical between the primary assembly and an alternate locus can result in multiple variant calls against regions of the primary assembly. In WGS analysis, this results in characteristic and recognizable patterns of variant calls at positions that we term alignable scaffold-discrepant positions (ASDPs). In 121 in-house genomes, on average 51.8 ± 3.8 of the 178 regions were found to correspond best to an alternate locus rather than the primary assembly sequence, and filtering these genomes with our algorithm led to the identification of 7863 variant calls per genome that colocalized with ASDPs.
    [Show full text]
  • Galaxy Platform for NGS Data Analyses
    Galaxy Platform For NGS Data Analyses Weihong Yan [email protected] Collaboratory Web Site http://qcb.ucla.edu/collaboratory Collaboratory Workshops Workshop Outline ü Day 1 § UCLA galaxy and user account § Galaxy web interface and management § Tools for NGS analyses and their application § Data formats § Build/share workflow and history § Q and A ü Day 2 § Galaxy Tools for RNA-seq analysis § Galaxy Tools for ChIP-seq analysis § Galaxy Tools for annotation. § Q and A *** Published datasets/results will be used in the tutorial UCLA Galaxy http://galaxy.hoffman2.idre.ucla.edu ü Hardware – Headnode (1) 96Gb memory, 12 core – Computing nodes (8) 48Gb memory, 12 core – Storage 100 Tb disk space ü Galaxy Resource Management - Hoffman2 grid engine Default: 1 core/job bowtie, bwa, tophat, cuffdiff, cufflinks, gatk programs: 4 core/job UCLA Galaxy http://galaxy.hoffman2.idre.ucla.edu ü galaxy login account: login: your email associated with ucla ü Disk quota: 1 Tb/user Galaxy Account Management Installed tools Launch analysis and view result History of execu7on and results Raw Reads *_qseq.txt, *.fastq Upload to Galaxy File transfer protocol (ftp) deMultiplex Barcode splitter, deMultiplex workflow fastqc, compute quality statistics, Quality Assessment draw quality score boxplot, draw nuclotides distribution Process Reads Trim sequences, sickle, scythe Alignment to bwa, bowtie, bowtie2, tophat Reference Format Conversion Text manipulation toolkit, BEDTools, SAM Results (sam/bam) Tools, java genomics toolkit, picard toolkit Downstream Analyses BS-Seeker2, cufflinks, cuffdiff, macs, macs2, GATK, CEAS Visualization Genome browser, IGV Repositories of Galaxy Tools https://toolshed.g2.bx.psu.edu ü History panel contains all datasets that are uploaded and results derived from certain analyses ü A history can be organized, annotated, and managed as a project ü History is sharable.
    [Show full text]
  • BMC Bioinformatics Biomed Central
    BMC Bioinformatics BioMed Central Database Open Access Atlas – a data warehouse for integrative bioinformatics Sohrab P Shah, Yong Huang, Tao Xu, Macaire MS Yuen, John Ling and BF Francis Ouellette* Address: UBC Bioinformatics Centre, University of British Columbia, Vancouver, BC, Canada Email: Sohrab P Shah - [email protected]; Yong Huang - [email protected]; Tao Xu - [email protected]; Macaire MS Yuen - [email protected]; John Ling - [email protected]; BF Francis Ouellette* - [email protected] * Corresponding author Published: 21 February 2005 Received: 04 September 2004 Accepted: 21 February 2005 BMC Bioinformatics 2005, 6:34 doi:10.1186/1471-2105-6-34 This article is available from: http://www.biomedcentral.com/1471-2105/6/34 © 2005 Shah et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description: The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs).
    [Show full text]
  • An Online Visualization Tool for Functional Features of Human Fusion Genes Pora Kim 1,*,†,Keyiya2,*,† and Xiaobo Zhou 1,3,4,*
    Published online 18 May 2020 Nucleic Acids Research, 2020, Vol. 48, Web Server issue W313–W320 doi: 10.1093/nar/gkaa364 FGviewer: an online visualization tool for functional features of human fusion genes Pora Kim 1,*,†,KeYiya2,*,† and Xiaobo Zhou 1,3,4,* 1School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA, 2College of Electronic and Information Engineering, Tongji University, Shanghai, China, 3McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA and 4School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA Received March 16, 2020; Revised April 17, 2020; Editorial Decision April 27, 2020; Accepted April 27, 2020 ABSTRACT broken gene context provided the aberrant functional clues to study disease genesis and there are many fusion genes Among the diverse location of the breakpoints (BPs) that have been recognized as biomarkers and therapeutic of structural variants (SVs), the breakpoints of fu- targets in cancer (1). Many tumorigenic FGs have retained sion genes (FGs) are located in the gene bodies. or lost oncogenic protein-domains or regulatory features This broken gene context provided the aberrant func- (2). The maintenance or loss of the functional features tional clues to study disease genesis. Many tumori- directly impacts on tumor initiation, progression, and genic fusion genes have retained or lost functional evolution. To date, there are multiple representative func- or regulatory domains and these features impacted tional mechanisms of fusion genes studied as shown in tumorigenesis. Full annotation of fusion genes aided Figure 1.
    [Show full text]
  • Gffread and Gffcompare[Version 1; Peer Review: 3 Approved]
    F1000Research 2020, 9:304 Last updated: 10 SEP 2020 SOFTWARE TOOL ARTICLE GFF Utilities: GffRead and GffCompare [version 1; peer review: 3 approved] Geo Pertea1,2, Mihaela Pertea 1,2 1Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21218, USA 2Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA v1 First published: 28 Apr 2020, 9:304 Open Peer Review https://doi.org/10.12688/f1000research.23297.1 Latest published: 09 Sep 2020, 9:304 https://doi.org/10.12688/f1000research.23297.2 Reviewer Status Abstract Invited Reviewers Summary: GTF (Gene Transfer Format) and GFF (General Feature Format) are popular file formats used by bioinformatics programs to 1 2 3 represent and exchange information about various genomic features, such as gene and transcript locations and structure. GffRead and version 2 GffCompare are open source programs that provide extensive and (revision) efficient solutions to manipulate files in a GTF or GFF format. While 09 Sep 2020 GffRead can convert, sort, filter, transform, or cluster genomic features, GffCompare can be used to compare and merge different version 1 gene annotations. 28 Apr 2020 report report report Availability and implementation: GFF utilities are implemented in C++ for Linux and OS X and released as open source under an MIT 1. Andreas Stroehlein , The University of license (https://github.com/gpertea/gffread, https://github.com/gpertea/gffcompare). Melbourne, Parkville, Australia Keywords 2. Michael I. Love , University of North gene annotation, transcriptome analysis, GTF and GFF file formats Carolina-Chapel Hill, Chapel Hill, USA 3. Rob Patro, University of Maryland, College This article is included in the International Park, USA Society for Computational Biology Community Any reports and responses or comments on the Journal gateway.
    [Show full text]
  • Next-Generation DNA Sequencing Informatics, 2Nd Edition
    This is a free sample of content from Next-Generation DNA Sequencing Informatics, 2nd edition. Click here for more information on how to buy the book. Index Page references followed by f denote figures. Page references followed by t denote tables. A Needleman–Wunsch (NW) algorithm, 49, 54, 110–113 overview, 109–110 Abeel, Thomas, 103 – – – ABI. See Applied Biosystems Inc. Smith Waterman (SW) algorithm, 38, 49, 62 63, 111 113 Ab initio genome annotation, 172, 178, 180t–181t Splign, 182 – TopHat, 43, 182 ab1PeakReporter software, 52 53 – A-Bruijn graph, 133–134 Alignment score, FASTA, 64 65 ABySS (Assembly by Short Sequencing), 134, 142, 147–153 Allele, 52, 354 Allele frequency, 76, 94, 193 effect of k-mer size and minimum pair number on assembly, fi 148–149, 149f Allele-speci c expression, 155, 298 overview of, 147–148 ALLPATHS, 134 quality of assembly, 149–153, 150t, 151f–152f ALN format, 92 α transcriptome assembly (Trans-ABySS), 158t, 160–161, 166 -diversity indices, 319 – – AceView database, 294, 295f Alternative splicing, 182, 293 296, 294f 295f Acrylamide gels Altschul, Stephen, 65 capillary tube, 4 Amazon Elastic Compute Cloud (EC2), 43, 254, 300, 315, – Sanger sequencing and, 2, 3–4 362 364, 366, 369 – ACT, 179t Amino acids, pairwise comparisons, 48 49 Adapter removal, 37–39, 39f, 43 Amplicons, 8, 30, 89, 204, 309, 312 Adapter Removal program, 38 Amplicon Variant Analyzer, 101 Affine gaps, 42, 110, 111–112 AmpliSeq Cancer Panel (Ion Torrent), 206 Algorithms Annotation, 75. See also Genome annotation – – – alignment, 49, 109–124, 129, 223, 338, 344 ChIP-seq peak, 240 242, 255, 259, 262 263, 262f 263f – assembly, 59, 127–129, 133–134, 338 proteogenomics and, 327 328, 328f – database searching, 113–115 of variants, 208 212 development, 364 ANNOVAR, 211 DNA fragment/genome assembly, 127–129, 133–134, 142 Anthrax, 141 dynamic programming, 110–124 Anti-sense RNA, 281 file compression, 79 Application programming interface (API), 368 Golay error-correcting, 31 Applied Biosystems Inc.
    [Show full text]
  • Identifying Disease Genes
    Genomics for today • Cancer genomics • Reproductive health • Forensic genomics • Agrigenomics • Complex disease genomics • Microbial genomics • Genomics in Drug and development • and more …omics Data/File formats • File format, a format for encoding data for storage in a computer file which is a standardized file format • Storage, access, sharing, interpretation, security, etc. http://en.wikipedia.org/wiki/Data_format Bioinformatics for dummies http://www.dummies.com/how-to/content/bioinformatics-data-formats.html Scientific data formats 23andMe microarray track data Browser Extensible Data Format AB1 (Chromatogram files used by DNA sequencing instruments from Applied Biosystems) MINiML (MIAME Notation in Markup Language) ABCD (Access to Biological Collection Data) mini Protein Data Bank Format ABCDDNA (Access to Biological Collection Data DNA extension) MIQAS-TAB (Minimal Information for QTLs and Association Studies Tabular) ABCDEFG (Access to Biological Collection Data Extension For Geosciences) MITAB ACE (Sequence assembly format) mmCIF (macromolecular Crystallographic Information File) Affymetrix Raw Intensity Format Multiple Alignment Forma ARLEQUIN Project Format mzData (deprecated) Axt Alignment Format mzIdentML BAM (Binary compressed SAM format) mzML BED (Browser extensible display format describing genes and other features of DNA sequences) mzQuantML BEDgraph mzXML (deprecated) Big Browser Extensible Data Format NCD (Natural Collections Descriptions) Big Wiggle Format NDTF (Neurophysiology Data Translation Format) Binary Alignement
    [Show full text]
  • A Resource Optimized GATK 4 Based Open Source Variant Calling Workflow
    Bathke and Lühken BMC Bioinformatics (2021) 22:402 https://doi.org/10.1186/s12859-021-04317-y SOFTWARE Open Access OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow Jochen Bathke* and Gesine Lühken *Correspondence: [email protected] Abstract giessen.de Background: The advent of next generation sequencing has opened new avenues Institute of Animal Breeding and Genetics, for basic and applied research. One application is the discovery of sequence vari- Justus Liebig University ants causative of a phenotypic trait or a disease pathology. The computational task Gießen, Ludwigstraße 21, of detecting and annotating sequence diferences of a target dataset between a 35390 Gießen, Germany reference genome is known as "variant calling". Typically, this task is computationally involved, often combining a complex chain of linked software tools. A major player in this feld is the Genome Analysis Toolkit (GATK). The "GATK Best Practices" is a com- monly referred recipe for variant calling. However, current computational recommen- dations on variant calling predominantly focus on human sequencing data and ignore ever-changing demands of high-throughput sequencing developments. Furthermore, frequent updates to such recommendations are counterintuitive to the goal of ofering a standard workfow and hamper reproducibility over time. Results: A workfow for automated detection of single nucleotide polymorphisms and insertion-deletions ofers a wide range of applications in sequence annotation of model and non-model organisms. The introduced workfow builds on the GATK Best Practices, while enabling reproducibility over time and ofering an open, generalized computational architecture. The workfow achieves parallelized data evaluation and maximizes performance of individual computational tasks.
    [Show full text]
  • Tools and Algorithms in Bioinformatics GCBA815, Fall 2013
    Tools and Algorithms in Bioinformatics GCBA815, Fall 2013 Week-13: NextGen Sequence Analysis Demonstrators: Suleyman Vural, Li You, Sanjit Pandey Babu Guda Department of Genetics, Cell Biology and Anatomy University of Nebraska Medical Center __________________________________________________________________________________________________ 11/22/2013 GCBA 815 Published Genome-Wide Associations through 12/2012 Published GWA at p≤5X10-8 for 17 trait categories NHGRI GWA Catalog www.genome.gov/ GWAStudies www.ebi.ac.uk/fgpt/gwas/ 1 __________________________________________________________________________________________________ 11/22/2013 GCBA 815 Allele Frequency vs Effect size of rare and common variants __________________________________________________________________________________________________ 11/22/2013 GCBA 815 2 IUPAC codes for nucleotides __________________________________________________________________________________________________ 11/22/2013 GCBA 815 NGS Applications in Biosciences • Genome • Exome sequencing • Clinical sequencing, personalized medicine • Targeted genome sequencing (Ex: Ion torrent amplicons) • Whole genome sequencing • Transcriptome • Whole transcriptome analysis • Small RNA analysis (siRNA, lncRNA, miRNA) • Gene expression profiling for selected target genes • Metagenome • Sequencing together the genomes of a mixture of species • Example: Human gut microbiota or environmental samples • Epigenome • Chromatin Immunoprecipitation Sequencing (ChIP-Seq) • Methylation and chromatin remodeling studies __________________________________________________________________________________________________
    [Show full text]
  • An Efficient General-Purpose Program for Assigning Sequence Reads To
    featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features Yang Liao 1;2, Gordon K Smyth 1;3 and Wei Shi 1;2∗ 1Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, 2Department of Computing and Information Systems, 3Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia Abstract Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key in- formation required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great vari- ety of genomic analyses but has so far received relatively little attention in the liter- ature. We present featureCounts, a read summarization program suitable for count- ing reads generated from either RNA or genomic DNA sequencing experiments. fea- tureCounts implements highly efficient chromosome hashing and feature blocking tech- niques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with ei- ther single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. featureCounts is available under GNU General Pub- lic License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages. 1 Introduction Next-generation (next-gen) sequencing technologies are revolution-izing biology by pro- arXiv:1305.3347v2 [q-bio.GN] 14 Nov 2013 viding the ability to sequence DNA at unprecendented speed (Schuster, 2007; Metzker, 2009).
    [Show full text]
  • A Standard Variation File Format for Human Genome Sequences
    Reese et al. Genome Biology 2010, 11:R88 http://genomebiology.com/2010/11/8/R88 METHOD Open Access A standard variation file format for human genome sequences Martin G Reese1*, Barry Moore2, Colin Batchelor3, Fidel Salas1, Fiona Cunningham4, Gabor T Marth5, Lincoln Stein6, Paul Flicek4, Mark Yandell2, Karen Eilbeck7* Abstract Here we describe the Genome Variation Format (GVF) and the 10Gen dataset. GVF, an extension of Generic Feature Format version 3 (GFF3), is a simple tab-delimited format for DNA variant files, which uses Sequence Ontology to describe genome variation data. The 10Gen dataset, ten human genomes in GVF format, is freely available for com- munity analysis from the Sequence Ontology website and from an Amazon elastic block storage (EBS) snapshot for use in Amazon’s EC2 cloud computing environment. Background GVF [14] is an extension of the widely used Generic With the advent of personalized genomics we have seen Feature Format version 3 (GFF3) standard for describing the first examples of fully sequenced individuals [1-9]. genome annotation data. The GFF3 format [15] was Now, next generation sequencing technologies promise developed to permit the exchange and comparison of to radically increase the number of human sequences in gene annotations between different model organism thepublicdomain.Thesedatawillcomenotjustfrom databases [16]. GFF3 is based on the General Feature large sequencing centers, but also from individual Format (GFF), which was originally developed during laboratories. For reasons of resource economy, ‘variant the human genome project to compare human genome files’ rather than raw sequence reads or assembled gen- annotations [17]. Importantly, GFF3, unlike GFF, is omes are rapidly emerging as the common currency for typed using an ontology.
    [Show full text]