Improved Neural Network Based General-Purpose Lossless Compression Mohit Goyal, Kedar Tatwawadi, Shubham Chandak, Idoia Ochoa
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Contrasting the Performance of Compression Algorithms on Genomic Data
Contrasting the Performance of Compression Algorithms on Genomic Data Cornel Constantinescu, IBM Research Almaden Outline of the Talk: • Introduction / Motivation • Data used in experiments • General purpose compressors comparison • Simple Improvements • Special purpose compression • Transparent compression – working on compressed data (prototype) • Parallelism / Multithreading • Conclusion Introduction / Motivation • Despite the large number of research papers and compression algorithms proposed for compressing genomic data generated by sequencing machines, by far the most commonly used compression algorithm in the industry for FASTQ data is gzip. • The main drawbacks of the proposed alternative special-purpose compression algorithms are: • slow speed of either compression or decompression or both, and also their • brittleness by making various limiting assumptions about the input FASTQ format (for example, the structure of the headers or fixed lengths of the records [1]) in order to further improve their specialized compression. 1. Ibrahim Numanagic, James K Bonfield, Faraz Hach, Jan Voges, Jorn Ostermann, Claudio Alberti, Marco Mattavelli, and S Cenk Sahinalp. Comparison of high-throughput sequencing data compression tools. Nature Methods, 13(12):1005–1008, October 2016. Fast and Efficient Compression of Next Generation Sequencing Data 2 2 General Purpose Compression of Genomic Data As stated earlier, gzip/zlib compression is the method of choice by the industry for FASTQ genomic data. FASTQ genomic data is a text-based format (ASCII readable text) for storing a biological sequence and the corresponding quality scores. Each sequence letter and quality score is encoded with a single ASCII character. FASTQ data is structured in four fields per record (a “read”). The first field is the SEQUENCE ID or the header of the read. -
Pack, Encrypt, Authenticate Document Revision: 2021 05 02
PEA Pack, Encrypt, Authenticate Document revision: 2021 05 02 Author: Giorgio Tani Translation: Giorgio Tani This document refers to: PEA file format specification version 1 revision 3 (1.3); PEA file format specification version 2.0; PEA 1.01 executable implementation; Present documentation is released under GNU GFDL License. PEA executable implementation is released under GNU LGPL License; please note that all units provided by the Author are released under LGPL, while Wolfgang Ehrhardt’s crypto library units used in PEA are released under zlib/libpng License. PEA file format and PCOMPRESS specifications are hereby released under PUBLIC DOMAIN: the Author neither has, nor is aware of, any patents or pending patents relevant to this technology and do not intend to apply for any patents covering it. As far as the Author knows, PEA file format in all of it’s parts is free and unencumbered for all uses. Pea is on PeaZip project official site: https://peazip.github.io , https://peazip.org , and https://peazip.sourceforge.io For more information about the licenses: GNU GFDL License, see http://www.gnu.org/licenses/fdl.txt GNU LGPL License, see http://www.gnu.org/licenses/lgpl.txt 1 Content: Section 1: PEA file format ..3 Description ..3 PEA 1.3 file format details ..5 Differences between 1.3 and older revisions ..5 PEA 2.0 file format details ..7 PEA file format’s and implementation’s limitations ..8 PCOMPRESS compression scheme ..9 Algorithms used in PEA format ..9 PEA security model .10 Cryptanalysis of PEA format .12 Data recovery from -
Metadefender Core V4.12.2
MetaDefender Core v4.12.2 © 2018 OPSWAT, Inc. All rights reserved. OPSWAT®, MetadefenderTM and the OPSWAT logo are trademarks of OPSWAT, Inc. All other trademarks, trade names, service marks, service names, and images mentioned and/or used herein belong to their respective owners. Table of Contents About This Guide 13 Key Features of Metadefender Core 14 1. Quick Start with Metadefender Core 15 1.1. Installation 15 Operating system invariant initial steps 15 Basic setup 16 1.1.1. Configuration wizard 16 1.2. License Activation 21 1.3. Scan Files with Metadefender Core 21 2. Installing or Upgrading Metadefender Core 22 2.1. Recommended System Requirements 22 System Requirements For Server 22 Browser Requirements for the Metadefender Core Management Console 24 2.2. Installing Metadefender 25 Installation 25 Installation notes 25 2.2.1. Installing Metadefender Core using command line 26 2.2.2. Installing Metadefender Core using the Install Wizard 27 2.3. Upgrading MetaDefender Core 27 Upgrading from MetaDefender Core 3.x 27 Upgrading from MetaDefender Core 4.x 28 2.4. Metadefender Core Licensing 28 2.4.1. Activating Metadefender Licenses 28 2.4.2. Checking Your Metadefender Core License 35 2.5. Performance and Load Estimation 36 What to know before reading the results: Some factors that affect performance 36 How test results are calculated 37 Test Reports 37 Performance Report - Multi-Scanning On Linux 37 Performance Report - Multi-Scanning On Windows 41 2.6. Special installation options 46 Use RAMDISK for the tempdirectory 46 3. Configuring Metadefender Core 50 3.1. Management Console 50 3.2. -
User Commands GZIP ( 1 ) Gzip, Gunzip, Gzcat – Compress Or Expand Files Gzip [ –Acdfhllnnrtvv19 ] [–S Suffix] [ Name ... ]
User Commands GZIP ( 1 ) NAME gzip, gunzip, gzcat – compress or expand files SYNOPSIS gzip [–acdfhlLnNrtvV19 ] [– S suffix] [ name ... ] gunzip [–acfhlLnNrtvV ] [– S suffix] [ name ... ] gzcat [–fhLV ] [ name ... ] DESCRIPTION Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77). Whenever possible, each file is replaced by one with the extension .gz, while keeping the same ownership modes, access and modification times. (The default extension is – gz for VMS, z for MSDOS, OS/2 FAT, Windows NT FAT and Atari.) If no files are specified, or if a file name is "-", the standard input is compressed to the standard output. Gzip will only attempt to compress regular files. In particular, it will ignore symbolic links. If the compressed file name is too long for its file system, gzip truncates it. Gzip attempts to truncate only the parts of the file name longer than 3 characters. (A part is delimited by dots.) If the name con- sists of small parts only, the longest parts are truncated. For example, if file names are limited to 14 characters, gzip.msdos.exe is compressed to gzi.msd.exe.gz. Names are not truncated on systems which do not have a limit on file name length. By default, gzip keeps the original file name and timestamp in the compressed file. These are used when decompressing the file with the – N option. This is useful when the compressed file name was truncated or when the time stamp was not preserved after a file transfer. Compressed files can be restored to their original form using gzip -d or gunzip or gzcat. -
Genomic Data Compression
Genomic data compression S. Cenk Sahinalp Bogaz’da Yaz Okulu 2018 Genome&storage&and&communication:&the&need • Research:)massive)genome)projects (e.g.)PCAWG))require)to)exchange) 10000s)of)genomes. • Need)to)cover)>200)cancer)types,)many)subtypes. • Within)PCAWG)TCGA)to)sequence)11K)patients)covering)33)cancer) types.)ICGC)to)cover)50)cancer)types)>15PB)data)at)The)Cancer) Genome)Collaboratory • Clinic:)$100s/genome (e.g.)NovaSeq))enable)sequencing)to)be)a) standard)tool)for)pathology • PCAWG)estimates)that)250M+)individuals)will)be)sequenced)by)2030 Current'needs • Typical(technology:(Illumina NovaSeq 1009400(bp reads,(2509500GB( uncompressed(data(for(high(coverage human(genome,(high(redundancy • 40%(of(the(human(genome(is(repetitive((mobile(genetic(elements,( centromeric DNA,(segmental(duplications,(etc.) • Upload/download:(55(hrs on(a(10Mbit(consumer(line;(5.5(hrs on(a( 100Mbit(high(speed(connection • Technologies(under(development:(expensive,(longer(reads,(higher(error( (PacBio,(Nanopore)(– lower(redundancy(and(higher(error(rates(limit( compression File%formats • Raw read'data:'FASTQ/FASTA'– dominant'fields:'(read'name,'sequence,' quality'score) • Mapped read'data:'SAM/BAM'– reads'reordered'based'on'mapping' locus'on'a'reference genome'(not'suitaBle'for'metagenomics,'organisms' with'no'reference) • Key'decisions'to'Be'made: • Each'format'can'Be'compressed'through'specialized'methods'– should' there'Be'a'standardized'format'for'compressed'genomes? • Better'file'formats'Based'on'mapping'loci'on'sequence'graphs' representing'common'variants'in'a'panJgenomic'reference? -
The Ark Handbook
The Ark Handbook Matt Johnston Henrique Pinto Ragnar Thomsen The Ark Handbook 2 Contents 1 Introduction 5 2 Using Ark 6 2.1 Opening Archives . .6 2.1.1 Archive Operations . .6 2.1.2 Archive Comments . .6 2.2 Working with Files . .7 2.2.1 Editing Files . .7 2.3 Extracting Files . .7 2.3.1 The Extract dialog . .8 2.4 Creating Archives and Adding Files . .8 2.4.1 Compression . .9 2.4.2 Password Protection . .9 2.4.3 Multi-volume Archive . 10 3 Using Ark in the Filemanager 11 4 Advanced Batch Mode 12 5 Credits and License 13 Abstract Ark is an archive manager by KDE. The Ark Handbook Chapter 1 Introduction Ark is a program for viewing, extracting, creating and modifying archives. Ark can handle vari- ous archive formats such as tar, gzip, bzip2, zip, rar, 7zip, xz, rpm, cab, deb, xar and AppImage (support for certain archive formats depends on the appropriate command-line programs being installed). In order to successfully use Ark, you need KDE Frameworks 5. The library libarchive version 3.1 or above is needed to handle most archive types, including tar, compressed tar, rpm, deb and cab archives. To handle other file formats, you need the appropriate command line programs, such as zipinfo, zip, unzip, rar, unrar, 7z, lsar, unar and lrzip. 5 The Ark Handbook Chapter 2 Using Ark 2.1 Opening Archives To open an archive in Ark, choose Open... (Ctrl+O) from the Archive menu. You can also open archive files by dragging and dropping from Dolphin. -
Arrow: Integration to 'Apache' 'Arrow'
Package ‘arrow’ September 5, 2021 Title Integration to 'Apache' 'Arrow' Version 5.0.0.2 Description 'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library. Depends R (>= 3.3) License Apache License (>= 2.0) URL https://github.com/apache/arrow/, https://arrow.apache.org/docs/r/ BugReports https://issues.apache.org/jira/projects/ARROW/issues Encoding UTF-8 Language en-US SystemRequirements C++11; for AWS S3 support on Linux, libcurl and openssl (optional) Biarch true Imports assertthat, bit64 (>= 0.9-7), methods, purrr, R6, rlang, stats, tidyselect, utils, vctrs RoxygenNote 7.1.1.9001 VignetteBuilder knitr Suggests decor, distro, dplyr, hms, knitr, lubridate, pkgload, reticulate, rmarkdown, stringi, stringr, testthat, tibble, withr Collate 'arrowExports.R' 'enums.R' 'arrow-package.R' 'type.R' 'array-data.R' 'arrow-datum.R' 'array.R' 'arrow-tabular.R' 'buffer.R' 'chunked-array.R' 'io.R' 'compression.R' 'scalar.R' 'compute.R' 'config.R' 'csv.R' 'dataset.R' 'dataset-factory.R' 'dataset-format.R' 'dataset-partition.R' 'dataset-scan.R' 'dataset-write.R' 'deprecated.R' 'dictionary.R' 'dplyr-arrange.R' 'dplyr-collect.R' 'dplyr-eval.R' 'dplyr-filter.R' 'expression.R' 'dplyr-functions.R' 1 2 R topics documented: 'dplyr-group-by.R' 'dplyr-mutate.R' 'dplyr-select.R' 'dplyr-summarize.R' -
Bandizip Professional Enterprise V710 Patchserialszip
1 / 2 Bandizip Professional Enterprise V7.10 Patch-Serials.zip Jun 17, 2021 — Bandizip Enterprise 7.17 Crack 2021 is strong archiver which gives you an ... Bandizip Professional 7.17 Crack + Keygen Free Download 2021 ... It also has support for split compression to certain sizes, such as 10MB or 700MB. ... all kinds of file compression software including WinZip, WinRAR, and 7-Zip.. Sep 8, 2020 — Bandizip Professional & Enterprise v7.10 + Patch-Serials ... BandiZip is an intuitive and fast archiving application that supports WinZip, 7-Zip, .... Mar 31, 2021 — IDM Crack 6.38 Build 19 Patch + Serial Key 2021 [Latest] Free ... VueScan Pro 9.7.51 Crack + Serial Number 2021 64/32Bit ... Torrent 2021: 1Password – Password Manager v7.7.4 Crack + Activation Code. ... [Latest-2021]: Bandizip Enterprise 7.15 Crack is managing zip files in multiple ZIP & 7Z formats.. Installing Windows OS components/upgrades/patches/fixes/drivers. /tools may ... SyncToy v2.1 64-bit for Windows XP Professional/Vista/7 64-bit. (x64) [3.46 MB] .... Bandizip Professional & Enterprise V7.10 + Patch-Serials [ha.. 6 months, Software, 9, 9.10 MB, 1, 0. Magnet Link · Secret Disk Professional V2020.03 Final + .... Apr 3, 2020 — Bandizip has a very fast Zip algorithm for compression & extraction with ... Supported OS: Windows Vista/7/8/10 (x86/x64/ARM64); License: ... Professional and Enterprise. ... Visible serial keys are not allowed even in images.. Mar 6, 2021 — Bandizip Crack is the name of a new, professional program, that ... Bandizip Enterprise 7.15 Crack with Serial Key Free Download: BandiZip Crack is an intuitive and fast archiving app that supports WinZip, 7-Zip, and WinRAR, as well as .. -
Kafl: Hardware-Assisted Feedback Fuzzing for OS Kernels
kAFL: Hardware-Assisted Feedback Fuzzing for OS Kernels Sergej Schumilo1, Cornelius Aschermann1, Robert Gawlik1, Sebastian Schinzel2, Thorsten Holz1 1Ruhr-Universität Bochum, 2Münster University of Applied Sciences Motivation IJG jpeg libjpeg-turbo libpng libtiff mozjpeg PHP Mozilla Firefox Internet Explorer PCRE sqlite OpenSSL LibreOffice poppler freetype GnuTLS GnuPG PuTTY ntpd nginx bash tcpdump JavaScriptCore pdfium ffmpeg libmatroska libarchive ImageMagick BIND QEMU lcms Adobe Flash Oracle BerkeleyDB Android libstagefright iOS ImageIO FLAC audio library libsndfile less lesspipe strings file dpkg rcs systemd-resolved libyaml Info-Zip unzip libtasn1OpenBSD pfctl NetBSD bpf man mandocIDA Pro clamav libxml2glibc clang llvmnasm ctags mutt procmail fontconfig pdksh Qt wavpack OpenSSH redis lua-cmsgpack taglib privoxy perl libxmp radare2 SleuthKit fwknop X.Org exifprobe jhead capnproto Xerces-C metacam djvulibre exiv Linux btrfs Knot DNS curl wpa_supplicant Apple Safari libde265 dnsmasq libbpg lame libwmf uudecode MuPDF imlib2 libraw libbson libsass yara W3C tidy- html5 VLC FreeBSD syscons John the Ripper screen tmux mosh UPX indent openjpeg MMIX OpenMPT rxvt dhcpcd Mozilla NSS Nettle mbed TLS Linux netlink Linux ext4 Linux xfs botan expat Adobe Reader libav libical OpenBSD kernel collectd libidn MatrixSSL jasperMaraDNS w3m Xen OpenH232 irssi cmark OpenCV Malheur gstreamer Tor gdk-pixbuf audiofilezstd lz4 stb cJSON libpcre MySQL gnulib openexr libmad ettercap lrzip freetds Asterisk ytnefraptor mpg123 exempi libgmime pev v8 sed awk make -
Is It Time to Replace Gzip?
bioRxiv preprint doi: https://doi.org/10.1101/642553; this version posted May 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Is it time to replace gzip? Comparison of modern compressors for molecular sequence databases Kirill Kryukov*, Mahoko Takahashi Ueda, So Nakagawa, Tadashi Imanishi Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan. *Correspondence: [email protected] Abstract Nearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for more efficient compression tool. We systematically benchmarked the available compressors on representative DNA, RNA and Protein datasets. We tested specialized sequence compressors 2bit, BLAST, DNA-COMPACT, DELIMINATE, Leon, MFCompress, NAF, UHT and XM, and general-purpose compressors brotli, bzip2, gzip, lz4, lzop, lzturbo, pbzip2, pigz, snzip, xz, zpaq and zstd. Overall, NAF and zstd performed well in terms of transfer/decompression speed. However, checking benchmark results is necessary when choosing compressor for specific data type and application. Benchmark results database is available at: http://kirr.dyndns.org/sequence-compression-benchmark/. Keywords: compression; benchmark; DNA; RNA; protein; genome; sequence; database. Molecular sequence databases store and distribute DNA, RNA and protein sequences as compressed FASTA files. Currently, nearly all databases universally depend on gzip for compression. This incredible longevity of the 26-year-old compressor probably owes to multiple factors, including conservatism of database operators, wide availability of gzip, and its generally acceptable performance. -
Rule Base with Frequent Bit Pattern and Enhanced K-Medoid Algorithm for the Evaluation of Lossless Data Compression
Volume 3, No. 1, Jan-Feb 2012 ISSN No. 0976-5697 International Journal of Advanced Research in Computer Science RESEARCH PAPER Available Online at www.ijarcs.info Rule Base with Frequent Bit Pattern and Enhanced k-Medoid Algorithm for the Evaluation of Lossless Data Compression. Nishad P.M.* Dr. N. Nalayini Ph.D Scholar, Department Of Computer Science Associate professor, Department of computer science NGM NGM College, Pollachi, India College Pollachi, Coimbatore, India [email protected] [email protected] Abstract: This paper presents a study of various lossless compression algorithms; to test the performance and the ability of compression of each algorithm based on ten different parameters. For evaluation the compression ratios of each algorithm on different parameters are processed. To classify the algorithms based on the compression ratio, rule base is constructed to mine with frequent bit pattern to analyze the variations in various compression algorithms. Also, enhanced K- Medoid clustering is used to cluster the various data compression algorithms based on various parameters. The cluster falls dissentingly high to low after the enhancement. The framed rule base consists of 1,048,576 rules, which is used to evaluate the compression algorithm. Two hundred and eleven Compression algorithms are used for this study. The experimental result shows only few algorithm satisfies the range “High” for more number of parameters. Keywords: Lossless compression, parameters, compression ratio, rule mining, frequent bit pattern, K–Medoid, clustering. I. INTRODUCTION the maximum shows the peek compression ratio of algorithms on various parameters, for example 19.43 is the Data compression is a method of encoding rules that minimum compression ratio and the 76.84 is the maximum allows substantial reduction in the total number of bits to compression ratio for the parameter EXE shown in table-1 store or transmit a file. -
Answers to Exercises
Answers to Exercises A bird does not sing because he has an answer, he sings because he has a song. —Chinese Proverb Intro.1: abstemious, abstentious, adventitious, annelidous, arsenious, arterious, face- tious, sacrilegious. Intro.2: When a software house has a popular product they tend to come up with new versions. A user can update an old version to a new one, and the update usually comes as a compressed file on a floppy disk. Over time the updates get bigger and, at a certain point, an update may not fit on a single floppy. This is why good compression is important in the case of software updates. The time it takes to compress and decompress the update is unimportant since these operations are typically done just once. Recently, software makers have taken to providing updates over the Internet, but even in such cases it is important to have small files because of the download times involved. 1.1: (1) ask a question, (2) absolutely necessary, (3) advance warning, (4) boiling hot, (5) climb up, (6) close scrutiny, (7) exactly the same, (8) free gift, (9) hot water heater, (10) my personal opinion, (11) newborn baby, (12) postponed until later, (13) unexpected surprise, (14) unsolved mysteries. 1.2: A reasonable way to use them is to code the five most-common strings in the text. Because irreversible text compression is a special-purpose method, the user may know what strings are common in any particular text to be compressed. The user may specify five such strings to the encoder, and they should also be written at the start of the output stream, for the decoder’s use.