SAMStat 2: quality control for next generation sequencing data.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 01 2023
01 01 2023
Historique:
received:
14
07
2022
revised:
04
11
2022
accepted:
12
01
2023
pubmed:
14
1
2023
medline:
21
1
2023
entrez:
13
1
2023
Statut:
ppublish
Résumé
SAMStat is an efficient program to extract quality control metrics from fastq and SAM/BAM files. A distinguishing feature is that it displays sequence composition, base quality composition and mapping error profiles split by mapping quality. This allows users to rapidly identify reasons for poor mapping including the presence of untrimmed adapters or poor sequencing quality at individual read positions. Here, we present a major update to SAMStat. The new version now supports paired-end and long-read data. Quality control plots are drawn using the ploty javascript library. The source code of SAMStat and code to reproduce the results are found here: https://github.com/timolassmann/samstat.
Identifiants
pubmed: 36637208
pii: 6986964
doi: 10.1093/bioinformatics/btad019
pmc: PMC9850270
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Feilman and Stan Perron Foundation
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press.
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