SAMtools
The standard toolkit for SAM/BAM/CRAM alignment files
SAMtools is the de facto standard for working with sequence alignments. Built on HTSlib, it is a near-universal dependency of genomics pipelines.
Common commands
1samtools sort input.bam -o sorted.bam2samtools index sorted.bam3samtools view -q 30 -b sorted.bam chr1:1-100000 > region.bam4samtools flagstat sorted.bam
Pairs naturally with BCFtools for variant data and minimap2 / BWA-MEM2 for alignment.
Related tools
Open source
Open source
Genomics & Sequencing
minimap2
Versatile long- and short-read sequence aligner
Command linePython library
Open source