Description

A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit

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Tools

biscuit Documentation

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

https://github.com/huishenlab/biscuitLicense: MIT

samblaster Documentation

samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. By default, samblaster reads SAM input from stdin and writes SAM to stdout.

doi: 10.1093/bioinformatics/btu314License: MIT

samtools Documentation

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

doi: 10.1093/bioinformatics/btp352License: MIT
Authors