{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T07:02:25Z","timestamp":1772521345958,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T00:00:00Z","timestamp":1752537600000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["R01HG009937"],"award-info":[{"award-number":["R01HG009937"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CCF-1750472"],"award-info":[{"award-number":["CCF-1750472"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CNS-1763680"],"award-info":[{"award-number":["CNS-1763680"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["252586"],"award-info":[{"award-number":["252586"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2024342821"],"award-info":[{"award-number":["2024342821"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chan Zuckerberg Initiative DAF"},{"DOI":"10.13039\/100000923","name":"Silicon Valley Community Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000923","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chan Zuckerberg Initiative Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenomic analyses with minimal accuracy loss compared to alignment-based methods. However, applying pseudoalignment to large genomic references, like chromosomes, is challenging due to their size and repetitive sequences. We introduce a new and modified pseudoalignment scheme that partitions each reference into \u201cvirtual colors.\u201d These are essentially overlapping bins of fixed maximal extent on the reference sequences that are treated as distinct \u201ccolors\u201d from the perspective of the pseudoalignment algorithm. We apply this modified pseudoalignment procedure to process and map single-cell ATAC-seq data in our new tool alevin-fry-atac. We compare alevin-fry-atac to both Chromap and Cell Ranger ATAC. Alevin-fry-atac is highly scalable and, when using 32 threads, is 2.8 times faster than Chromap (the second fastest approach) while using only 33% of the memory required by Chromap. The resulting peaks and clusters generated from alevin-fry-atac show high concordance with those obtained from both Chromap and the Cell Ranger ATAC pipeline, demonstrating that virtual color-enhanced pseudoalignment directly to the genome provides a fast, memory-frugal, and accurate alternative to existing approaches for single-cell ATAC-seq processing. The development of alevin-fry-atac brings single-cell ATAC-seq processing into a unified ecosystem with single-cell RNA-seq processing (via alevin-fry) to work toward providing a truly open alternative to many of the varied capabilities of CellRanger.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Alevin-fry-atac is written in Rust and C++17, and is freely-available under a BSD 3-clause license. It is integrated into piscem (https:\/\/github.com\/COMBINE-lab\/piscem) and alevin-fry (https:\/\/github.com\/COMBINE-lab\/alevin-fry), and is also supported directly as part of simpleaf (https:\/\/github.com\/COMBINE-lab\/simpleaf)<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf234","type":"journal-article","created":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T13:02:25Z","timestamp":1752584545000},"page":"i237-i245","source":"Crossref","is-referenced-by-count":2,"title":["Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment"],"prefix":"10.1093","volume":"41","author":[{"given":"Noor Pratap","family":"Singh","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Maryland , College Park, MD 20742,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5129-9749","authenticated-orcid":false,"given":"Jamshed","family":"Khan","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland , College Park, MD 20742,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8463-1675","authenticated-orcid":false,"given":"Rob","family":"Patro","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Maryland , College Park, MD 20742,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2025,7,15]]},"reference":[{"key":"2025071509021504700_btaf234-B1","doi-asserted-by":"crossref","first-page":"i260","DOI":"10.1093\/bioinformatics\/btad233","article-title":"Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes","volume":"39","author":"Alanko","year":"2023","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B2","doi-asserted-by":"crossref","first-page":"i169","DOI":"10.1093\/bioinformatics\/bty292","article-title":"A space and time-efficient index for the compacted colored de Bruijn graph","volume":"34","author":"Almodaresi","year":"2018","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B3","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1007\/978-3-030-32686-9_21","volume-title":"COBS: A Compact Bit-Sliced Signature Index","author":"Bingmann","year":"2019"},{"key":"2025071509021504700_btaf234-B4","author":"Booeshaghi","year":"2023"},{"key":"2025071509021504700_btaf234-B5","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat Biotechnol"},{"key":"2025071509021504700_btaf234-B6","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1186\/s13059-018-1568-0","article-title":"KrakenUniq: confident and fast metagenomics classification using unique k-mer counts","volume":"19","author":"Breitwieser","year":"2018","journal-title":"Genome Biol"},{"key":"2025071509021504700_btaf234-B7","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"Buenrostro","year":"2013","journal-title":"Nat Methods"},{"key":"2025071509021504700_btaf234-B8","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nature14590","article-title":"Single-cell chromatin accessibility reveals principles of regulatory variation","volume":"523","author":"Buenrostro","year":"2015","journal-title":"Nature"},{"key":"2025071509021504700_btaf234-B9","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1126\/science.aab1601","article-title":"Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing","volume":"348","author":"Cusanovich","year":"2015","journal-title":"Science"},{"key":"2025071509021504700_btaf234-B11","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13015-024-00251-9","article-title":"Fulgor: a fast and compact k-mer index for large-scale matching and color queries","volume":"19","author":"Fan","year":"2024","journal-title":"Algorithms Mol Biol"},{"key":"2025071509021504700_btaf234-B12","author":"Gaspar","year":"2018"},{"key":"2025071509021504700_btaf234-B13","doi-asserted-by":"crossref","first-page":"btad614","DOI":"10.1093\/bioinformatics\/btad614","article-title":"simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fry","volume":"39","author":"He","year":"2023","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B14","doi-asserted-by":"publisher","author":"He","year":"2023","DOI":"10.1101\/2023.01.04.522742"},{"key":"2025071509021504700_btaf234-B15","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/s41592-022-01408-3","article-title":"Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data","volume":"19","author":"He","year":"2022","journal-title":"Nat Methods"},{"key":"2025071509021504700_btaf234-B16","author":"Holtgrewe","year":"2010"},{"key":"2025071509021504700_btaf234-B17","doi-asserted-by":"crossref","first-page":"i177","DOI":"10.1093\/bioinformatics\/btab309","article-title":"Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections","volume":"37","author":"Khan","year":"2021","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B18","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2025071509021504700_btaf234-B19","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1126\/science.1256271","article-title":"Chromatin state dynamics during blood formation","volume":"345","author":"Lara-Astiaso","year":"2014","journal-title":"Science"},{"key":"2025071509021504700_btaf234-B20","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B21","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B22","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B23","doi-asserted-by":"publisher","author":"M\u00e4klin","DOI":"10.12688\/wellcomeopenres.15639.2"},{"key":"2025071509021504700_btaf234-B24","author":"Morrissey"},{"key":"2025071509021504700_btaf234-B25","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat Methods"},{"key":"2025071509021504700_btaf234-B26","doi-asserted-by":"publisher","author":"Patro","year":"2025","DOI":"10.5281\/zenodo.15096903"},{"key":"2025071509021504700_btaf234-B27","doi-asserted-by":"crossref","first-page":"i185","DOI":"10.1093\/bioinformatics\/btac245","article-title":"Sparse and skew hashing of k-mers","volume":"38","author":"Pibiri","year":"2022","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B28","author":"Picard Toolkit","year":"2019"},{"key":"2025071509021504700_btaf234-B29","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1038\/s41593-018-0079-3","article-title":"Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation","volume":"21","author":"Preissl","year":"2018","journal-title":"Nat Neurosci"},{"key":"2025071509021504700_btaf234-B30","doi-asserted-by":"crossref","first-page":"3363","DOI":"10.1093\/bioinformatics\/bth408","article-title":"Reducing storage requirements for biological sequence comparison","volume":"20","author":"Roberts","year":"2004","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B31","doi-asserted-by":"crossref","first-page":"2082","DOI":"10.1093\/bioinformatics\/btx106","article-title":"Pseudoalignment for metagenomic read assignment","volume":"33","author":"Schaeffer","year":"2017","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B32","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1101\/gr.192294.115","article-title":"Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions","volume":"25","author":"Schep","year":"2015","journal-title":"Genome Res"},{"key":"2025071509021504700_btaf234-B33","doi-asserted-by":"crossref","first-page":"btac845","DOI":"10.1093\/bioinformatics\/btac845","article-title":"KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping","volume":"39","author":"Shen","year":"2023","journal-title":"Bioinformatics"},{"key":"2025071509021504700_btaf234-B34","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/s13059-022-02610-4","article-title":"AGAMEMNON: an accurate metaGenomics and MEtatranscriptoMics quaNtificatiON analysis suite","volume":"23","author":"Skoufos","year":"2022","journal-title":"Genome Biol"},{"key":"2025071509021504700_btaf234-B35","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1186\/s13059-020-02151-8","article-title":"Alignment and mapping methodology influence transcript abundance estimation","volume":"21","author":"Srivastava","year":"2020","journal-title":"Genome Biol"},{"key":"2025071509021504700_btaf234-B36","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s13072-019-0260-2","article-title":"Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks","volume":"12","author":"Starks","year":"2019","journal-title":"Epigenet Chromatin"},{"key":"2025071509021504700_btaf234-B37","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1038\/s41592-021-01282-5","article-title":"Single-cell chromatin state analysis with Signac","volume":"18","author":"Stuart","year":"2021","journal-title":"Nat Methods"},{"key":"2025071509021504700_btaf234-B38","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1186\/s13059-020-02116-x","article-title":"Integrative analyses of single-cell transcriptome and regulome using MAESTRO","volume":"21","author":"Wang","year":"2020","journal-title":"Genome Biol"},{"key":"2025071509021504700_btaf234-B39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol"},{"key":"2025071509021504700_btaf234-B40","doi-asserted-by":"crossref","first-page":"6566","DOI":"10.1038\/s41467-021-26865-w","article-title":"Fast alignment and preprocessing of chromatin profiles with Chromap","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat Commun"},{"key":"2025071509021504700_btaf234-B41","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/Supplement_1\/i237\/63745515\/btaf234.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/Supplement_1\/i237\/63745515\/btaf234.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T13:02:30Z","timestamp":1752584550000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/41\/Supplement_1\/i237\/8199381"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,1]]},"references-count":40,"journal-issue":{"issue":"Supplement_1","published-print":{"date-parts":[[2025,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf234","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,7]]},"published":{"date-parts":[[2025,7,1]]}}}