{"doi":"10.1093/bioinformatics/bty189","title":"scanPAV: a pipeline for extracting presence–absence variations in genome pairs","abstract":"<jats:title>Abstract</jats:title>\n               <jats:sec>\n                  <jats:title>Motivation</jats:title>\n                  <jats:p>The recent technological advances in genome sequencing techniques have resulted in an exponential increase in the number of sequenced human and non-human genomes. The ever increasing number of assemblies generated by novel de novo pipelines and strategies demands the development of new software to evaluate assembly quality and completeness. One way to determine the completeness of an assembly is by detecting its Presence–Absence variations (PAV) with respect to a reference, where PAVs between two assemblies are defined as the sequences present in one assembly but entirely missing in the other one. Beyond assembly error or technology bias, PAVs can also reveal real genome polymorphism, consequence of species or individual evolution, or horizontal transfer from viruses and bacteria.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>We present scanPAV, a pipeline for pairwise assembly comparison to identify and extract sequences present in one assembly but not the other. In this note, we use the GRCh38 reference assembly to assess the completeness of six human genome assemblies from various assembly strategies and sequencing technologies including Illumina short reads, 10× genomics linked-reads, PacBio and Oxford Nanopore long reads, and Bionano optical maps. We also discuss the PAV polymorphism of seven Tasmanian devil whole genome assemblies of normal animal tissues and devil facial tumour 1 (DFT1) and 2 (DFT2) samples, and the identification of bacterial sequences as contamination in some of the tumorous assemblies.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation</jats:title>\n                  <jats:p>The pipeline is available under the MIT License at https://github.com/wtsi-hpag/scanPAV.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information</jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.</jats:p>\n               </jats:sec>","journal":"Bioinformatics","year":2018,"id":588922,"datarank":1.1977888065963582,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"self_citation_contribution":0.519860385419959,"citation_network_contribution":0.6779284211763993,"self_endowment_contribution":0.519860385419959,"citer_contribution":0.6779284211763993,"corpus_percentile":null,"corpus_rank":null,"citation_count":31,"citer_count":30,"citers_with_citation_signal":17,"citers_with_endowment":17,"datacite_reuse_total":25,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1506753,"name":"Maximilian R Stammnitz","orcid":null,"position":1,"is_corresponding":false},{"id":1506754,"name":"Elizabeth P Murchison","orcid":null,"position":2,"is_corresponding":false},{"id":550068,"name":"Zemin Ning","orcid":"0000-0003-4359-776X","position":3,"is_corresponding":false},{"id":1202335,"name":"Francesca Giordano","orcid":"0000-0003-0144-2081","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"scanPAV: a pipeline for extracting presence–absence variations in genome pairs","abstract":"<jats:title>Abstract</jats:title>\n               <jats:sec>\n                  <jats:title>Motivation</jats:title>\n                  <jats:p>The recent technological advances in genome sequencing techniques have resulted in an exponential increase in the number of sequenced human and non-human genomes. The ever increasing number of assemblies generated by novel de novo pipelines and strategies demands the development of new software to evaluate assembly quality and completeness. One way to determine the completeness of an assembly is by detecting its Presence–Absence variations (PAV) with respect to a reference, where PAVs between two assemblies are defined as the sequences present in one assembly but entirely missing in the other one. Beyond assembly error or technology bias, PAVs can also reveal real genome polymorphism, consequence of species or individual evolution, or horizontal transfer from viruses and bacteria.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>We present scanPAV, a pipeline for pairwise assembly comparison to identify and extract sequences present in one assembly but not the other. In this note, we use the GRCh38 reference assembly to assess the completeness of six human genome assemblies from various assembly strategies and sequencing technologies including Illumina short reads, 10× genomics linked-reads, PacBio and Oxford Nanopore long reads, and Bionano optical maps. We also discuss the PAV polymorphism of seven Tasmanian devil whole genome assemblies of normal animal tissues and devil facial tumour 1 (DFT1) and 2 (DFT2) samples, and the identification of bacterial sequences as contamination in some of the tumorous assemblies.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation</jats:title>\n                  <jats:p>The pipeline is available under the MIT License at https://github.com/wtsi-hpag/scanPAV.</jats:p>\n               </jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information</jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.</jats:p>\n               </jats:sec>","is_dataset_classified":null,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"datacite_reuse_total":25,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"29608694","pmcid":"PMC6129304","openalex_id":"https://openalex.org/W2794893153","authors":[],"funders":[{"funder_name":"Wellcome","grant_id":"WT098051","title":null},{"funder_name":"Wellcome","grant_id":"102942/Z/13/A","title":null},{"funder_name":"Wellcome Trust","grant_id":"102942","title":"Genome diversity and evolution in transmissible cancers in dogs and tasmanian devils"},{"funder_name":"Wellcome Trust","grant_id":"unidentified","title":"unidentified"},{"funder_name":"Wellcome Trust","grant_id":"098051","title":"Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers"},{"funder_name":"Leverhulme Trust","grant_id":"","title":null},{"funder_name":"Philip Leverhulme 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and Phylogenetic Studies","Genomic variations and chromosomal abnormalities","Bacteriophages and microbial interactions","0301 basic medicine","03 medical and health sciences","0206 medical engineering","02 engineering and technology","Animals","Chromosome Mapping","Genome","Genomics","High-Throughput Nucleotide Sequencing","Humans","Sequence Analysis, DNA","Software"],"mesh_terms":["Animals","Chromosome Mapping","Humans","Software","Genome","Sequence Analysis, DNA","Genomics","High-Throughput Nucleotide Sequencing"],"keywords":["Sequence assembly","Reference genome","Genome","Computational biology","Pipeline (software)","Nanopore sequencing","Genomics","Human genome","Pairwise comparison","Computer science","Biology","De Bruijn graph","Genetics","Gene","Theoretical computer science","Artificial intelligence","Programming language","Graph","Animals","Chromosome Mapping","High-Throughput Nucleotide Sequencing","Humans","Sequence Analysis, DNA","Applications 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