SAMStat

SAMStat is a C program which will generate a report with a variety of statistics on quality, read length, mapping, etc. The report is HTML5 formatted. It supports sam, bam, fasta, and fastq files.

This application is in the GRC module

module load grc

Usage is simple:

samstat file.bam

It also supports wild-cards and will produce a different report for each matching file:

samstat *.bam