Open-source tool for sequencing alignment files: viewing, sorting and statistics for SAM/BAM/CRAM.
SAMtools is an open-source tool for processing sequencing alignment files, used to view, convert, sort, index, summarise and filter SAM, BAM and CRAM files. It is one of the foundation tools of NGS analysis pipelines.
Use cases: BAM file processing, sequencing data, variant analysis, sorting and indexing, bioinformatics pipelines
Note: usually used with BWA, Bowtie2, BCFtools, FastQC and MultiQC.
