SAMStat 2: quality control for next generation sequencing data

Timo Lassmann

doi:10.1093/bioinformatics/btad019

SAMStat 2: quality control for next generation sequencing data

Bioinformatics. 2023 Jan 1;39(1):btad019. doi: 10.1093/bioinformatics/btad019.

Author

Timo Lassmann¹

Affiliation

¹ Precision Health, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia.

Abstract

Motivation: 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.

Results: 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.

Availability and implementation: The source code of SAMStat and code to reproduce the results are found here: https://github.com/timolassmann/samstat.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Composition
High-Throughput Nucleotide Sequencing*
Quality Control
Sequence Analysis, DNA / methods
Software*

Grants and funding

Feilman and Stan Perron Foundation