Resources

Resources

Links to software and publications with related and/or interesting features.

Sequencing data analysis toolkits

• Picard - several tools for modifying and analyzing alignment files

• NGSutils - toolkit for analyzing fastq and alignment files.

• Triagetools - toolkit for analyzing pre-alignment data
  (Disclaimer: shared developers between projects)

• Locsmoc - post-processing of genomic tracks.
  (Disclaimer: shared developers between projects)

Variant calling software

• GATK - variant calling and other features

• Varscan2 - variant calling and other features

Publications

• Comparing somatic mutation-callers: beyond Venn diagrams - a review of somatic variant calling software other than Bamformatics