SAMStat¶

Description¶

SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines. SAMStat reports nucleotide composition, length distribution, base quality distribution, mapping statistics, mismatch, insertion and deletion error profiles, di-nucleotide and 10-mer over-representation. The output is a single html5 page which can be interpreted by a non-specialist.

Environment Modules¶

Run module spider samstat to find out what environment modules are available for this application.

Environment Variables¶

HPC_SAMSTAT_DIR - installation directory
HPC_SAMSTAT_BIN - executable directory

Citation¶

If you publish research that uses samstat you have to cite it as follows:

Lassmann et al. (2010) "SAMStat: monitoring biases in next generation sequencing data." Bioinformatics doi:10.1093/bioinformatics/btq614 [PMID: 21088025]

Categories¶

biology, ngs, sequencing