SAMStat 2: quality control for next generation sequencing data.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 36637208.
- Also identified by DOI 10.1093/bioinformatics/btad019 and PMC identifier 9850270.
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Abstract
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.
Medical subject headings
- High-Throughput Nucleotide Sequencing
- Software