Keywords:
Base Composition; High-Throughput Nucleotide Sequencing; Quality Control; Sequence Analysis; DNA/methods; Software
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.