Compression of FASTQ and SAM Format Sequencing Data
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{"title"=>"Compression of FASTQ and SAM Format Sequencing Data", "type"=>"journal", "authors"=>[{"first_name"=>"James K.", "last_name"=>"Bonfield", "scopus_author_id"=>"6602684116"}, {"first_name"=>"Matthew V.", "last_name"=>"Mahoney", "scopus_author_id"=>"55630410400"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"368580439", "issn"=>"19326203", "isbn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0059190", "scopus"=>"2-s2.0-84875363204", "pmid"=>"23533605", "sgr"=>"84875363204"}, "id"=>"180b6d77-6615-3bf1-a13f-97e5c3338fec", "abstract"=>"Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzcomp, including the winning entry. These are compared against existing algorithms for both reference based compression (CRAM, Goby) and non-reference based compression (DSRC, BAM) and other recently published competition entries (Quip, SCALCE). The tools are shown to be the new Pareto frontier for FASTQ compression, offering state of the art ratios at affordable CPU costs. All programs are freely available on SourceForge. Fastqz: https://sourceforge.net/projects/fastqz/, fqzcomp: https://sourceforge.net/projects/fqzcomp/, and samcomp: https://sourceforge.net/projects/samcomp/.", "link"=>"http://www.mendeley.com/research/compression-fastq-sam-format-sequencing-data", "reader_count"=>139, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Librarian"=>1, "Researcher"=>46, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>38, "Student > Postgraduate"=>1, "Student > Master"=>16, "Other"=>4, "Student > Bachelor"=>10, "Lecturer"=>4, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Librarian"=>1, "Researcher"=>46, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>38, "Student > Postgraduate"=>1, "Student > Master"=>16, "Other"=>4, "Student > Bachelor"=>10, "Lecturer"=>4, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Agricultural and Biological Sciences"=>59, "Arts and Humanities"=>1, "Chemistry"=>1, "Computer Science"=>41, "Earth and Planetary Sciences"=>1, "Engineering"=>13, "Biochemistry, Genetics and Molecular Biology"=>10, "Materials Science"=>1, "Mathematics"=>2, "Medicine and Dentistry"=>4, "Physics and Astronomy"=>1, "Immunology and Microbiology"=>2, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>13}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>59}, "Computer Science"=>{"Computer Science"=>41}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}}, "reader_count_by_country"=>{"Netherlands"=>2, "Sweden"=>2, "United States"=>9, "China"=>2, "United Kingdom"=>4, "France"=>3, "Spain"=>3}, "group_count"=>16}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/995840"], "description"=>"<p>Each mark represents a different entry, coloured by author. Ibrahim Numanagic’s entry had a minor decoding problem causing a minority of read-names to mismatch. All other entries plotted here were lossless. The entries have been broken down into reference based (A) and non-reference based (B) solutions. A clear wall can be seen in the non-reference methods requiring exponential growth in CPU time for minor linear improvements in compression ratio.</p>", "links"=>[], "tags"=>["compression"], "article_id"=>658565, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["James K. Bonfield", "Matthew V. Mahoney"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059190.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SequenceSqueeze_results_real_time_vs_compression_ratio_/658565", "title"=>"SequenceSqueeze results: real time vs compression ratio.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-23 02:44:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/995841"], "description"=>"<p>SRR007215 is SOLiD data, SRR003177 is 454 data, while SRR02750 and SRR065390 are Illumina data at shallow and deep depths respectively. Not all programs support all types of data.</p>", "links"=>[], "tags"=>["ratios"], "article_id"=>658566, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["James K. Bonfield", "Matthew V. Mahoney"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059190.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_File_size_ratios_vs_real_time_to_compress_/658566", "title"=>"File size ratios vs real time to compress.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-23 02:45:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/995842"], "description"=>"<div><p>Storage and transmission of the data produced by modern DNA sequencing instruments has become a major concern, which prompted the Pistoia Alliance to pose the SequenceSqueeze contest for compression of FASTQ files. We present several compression entries from the competition, Fastqz and Samcomp/Fqzcomp, including the winning entry. These are compared against existing algorithms for both reference based compression (CRAM, Goby) and non-reference based compression (DSRC, BAM) and other recently published competition entries (Quip, SCALCE). The tools are shown to be the new Pareto frontier for FASTQ compression, offering state of the art ratios at affordable CPU costs. All programs are freely available on SourceForge. Fastqz: <a href=\"https://sourceforge.net/projects/fastqz/\" target=\"_blank\">https://sourceforge.net/projects/fastqz/</a>, fqzcomp: <a href=\"https://sourceforge.net/projects/fqzcomp/\" target=\"_blank\">https://sourceforge.net/projects/fqzcomp/</a>, and samcomp: <a href=\"https://sourceforge.net/projects/samcomp/\" target=\"_blank\">https://sourceforge.net/projects/samcomp/</a>.</p> </div>", "links"=>[], "tags"=>["compression", "fastq", "sam", "sequencing", "data"], "article_id"=>658567, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["James K. Bonfield", "Matthew V. Mahoney"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059190"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Compression_of_FASTQ_and_SAM_Format_Sequencing_Data__/658567", "title"=>"Compression of FASTQ and SAM Format Sequencing Data", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-23 02:45:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008028"], "description"=>"<p>The data sets used to test the compression tools along with the sequencing platforms that produced them. <i>Length</i> is the average sequence length. <i>Depth</i> is the average genome depth assuming 100% of sequences in the data set can be aligned.</p>", "links"=>[], "tags"=>["sets"], "article_id"=>668655, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["James K. Bonfield", "Matthew V. Mahoney"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059190.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Data_sets_used_for_program_evaluation_/668655", "title"=>"Data sets used for program evaluation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-22 02:24:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008045"], "description"=>"<p>Program version names, numbers and common command line options. Additional options were sometimes required to specify the name of the reference used, but this differed per data set.</p>", "links"=>[], "tags"=>["versions"], "article_id"=>668673, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["James K. Bonfield", "Matthew V. Mahoney"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059190.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Program_names_versions_and_options_/668673", "title"=>"Program names, versions and options.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-22 02:24:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008060"], "description"=>"<p>SRR003177 is 1.5 M human sequences of variable length (avg 564 bp); SRR07215_1 is 4.7 M human seqs of length 25 bp plus 1 primer base; SRR027520_1 is 24.2 M human seqs of length 76 bp; SRR065390_1 is 33.8 M C.Elegans seqs of length 100 bp. Ratio is the compressed size divided by the uncompressed size. C.R. and D.R. are compression and decompression rates in MB/s. (a) Program does not support variable length sequences. (b) Program does not support SOLiD data.</p>", "links"=>[], "tags"=>["rates"], "article_id"=>668687, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["James K. Bonfield", "Matthew V. Mahoney"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059190.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Compression_rates_and_ratios_/668687", "title"=>"Compression rates and ratios.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-22 02:24:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008077"], "description"=>"<p>Showing the compressed file size break down by bits per sequence identifier, per base-call and per quality value. In some cases these sizes refer to cases where a reference was previously used to map, but it has not been used during compression (e.g. BAM). The ID, Base and Qual columns are the number of bits required to store the complete sequence identifier, a single base nucleotide and a single quality value respectively. The C.R. column is the compression rate in MB per second. Mem is the amount of memory required during compression. References used were human hg19 and C.Elegans WS233. Non-reference based Quip used the “-a” assembly option for high compression mode.</p>a<p>Goby does not store unmapped data. The Goby figures have been estimated by adding 2 bits per absent base-call and scaling up the name and quality figures by the percentage of unmapped reads.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "computer science"], "article_id"=>668705, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["James K. Bonfield", "Matthew V. Mahoney"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059190.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Compression_by_data_type_/668705", "title"=>"Compression by data type.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-22 02:25:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1008088"], "description"=>"<p>Size of data components in the public SequenceSqueeze test set SRR062634 (6,345,444,769 bytes uncompressed).</p>", "links"=>[], "tags"=>["alignment"], "article_id"=>668719, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["James K. Bonfield", "Matthew V. Mahoney"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0059190.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fastqz_alignment_benchmarks_/668719", "title"=>"Fastqz alignment benchmarks.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-03-22 02:25:19"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Computer and information sciences/Computer software", "average_usage"=>[275, 441, 557, 690, 806, 929, 1029, 1117, 1218, 1286, 1349, 1438, 1506]}, {"subject_area"=>"/Physical sciences/Physics", "average_usage"=>[254, 421, 527, 626, 720, 813, 900, 983, 1063, 1136, 1210, 1283, 1342]}]}
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