{"doi":"10.1101/020024","title":"SAM/BAM format v1.5 extensions for\n                  <i>de novo</i>\n                  assemblies","abstract":"<h4>ABSTRACT</h4> <h4>Summary:</h4> The plain text Sequence Alignment/Map (SAM) file format and its companion binary form (BAM) are a generic alignment format for storing read alignments against reference sequences (and unmapped reads) together with structured meta-data (Li et al. , 2009). Driven by the needs of the 1000 Genomes Project which sequenced many individual human genomes, early SAM/BAM usage focused on pairwise alignments of reads to a reference. However, through the CIGAR P operator multiple sequence alignments can also be preserved. Herein we describe clarifications and additions in version 1.5 of the specification to facilitate storing de novo sequence alignments: Padded reference sequences (with gap characters), annotation of reads or regions of the reference, and the option of embedding the reference sequence within the file. <h4>Availability:</h4> The latest public release of the specification is at http://samtools.sourceforge.net/SAM1.pdf , with in development drafts at https://github.com/samtools/hts-specs/ under version control. <h4>Contact:</h4> peter.cock@hutton.ac.uk","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2015,"id":6491,"datarank":0.3596842909197557,"base_score":2.3978952727983707,"endowment":2.3978952727983707,"self_citation_contribution":0.3596842909197557,"citation_network_contribution":0.0,"self_endowment_contribution":0.3596842909197557,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":10,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.1066,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2015-05-29","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":15616,"name":"James K. Bonfield","orcid":"0000-0002-6447-4112","position":1,"is_corresponding":false},{"id":59613,"name":"Bastien Chevreux","orcid":"0000-0003-4419-8840","position":2,"is_corresponding":false},{"id":30887,"name":"Alexandra P. Lewis","orcid":"0000-0002-6195-4786","position":3,"is_corresponding":false},{"id":19140,"name":"Peter J. A. Cock","orcid":"0000-0001-9513-9993","position":0,"is_corresponding":true}],"reference_count":15,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}