biohazard-tools

This is a collection of command line utilities that do useful stuff involving BAM files for Next Generation Sequencing data:

• bam-fixpair: brings mates from paired end runs together and fixes their flags. Can also pipe into programs that expect two or three FastQ files as input.

• bam-mangle: filters BAM files through a flexible boolean expression language. A little bit like find (but not quite like awk) for BAM.

• bam-meld: melds multiple BAM files together, retaining only the best alignment for each read.

• bam-rewrap: wraps alignments around the origin of a circular reference. (Use this to get sensible alignments to mitochondria. bam-rmdup includes similar functionality.)

• bam-rmdup: removes PCR duplicates from BAM files and computes a consensus sequence for each cluster of replicates.

• expound: annotates regions, similar to what bedtools does, but expound has a neat client/server mode so it doesn't have to read the same annotation file over and over again.

• fastq2bam: converts FastQ to BAM. It handles many weird combinations of one to four input files and optionally trims reads and merges read pairs.

Installation

biohazard-tools uses Cabal, the standard installation mechanism for Haskell. It depends on the biohazard library and additional stuff from Hackage. To install, follow these steps:

• install GHC (see http://haskell.org/ghc) and Cabal (see http://haskell.org/cabal),
• run cabal update (takes a while to download the current package list),
• install Judy, either from http://judy.sourceforge.net, or through your package manager (it's named libjudy-dev or similar),
• run cabal install https://bitbucket.org/ustenzel/biohazard-tools/get/master.tar.gz (takes even longer).
• If you don't have or don't like Judy, you can install without it by running cabal install -f -judy https://bitbucket.org/ustenzel/biohazard/get/master.tar.gz https://bitbucket.org/ustenzel/biohazard-tools/get/master.tar.gz. The performance of expound may suffer a bit.

When done, on an unmodified Cabal setup, you will find the binaries in ${HOME}/cabal/bin. Cabal can install them in a different place, please refer to the Cabal documentation at http://www.haskell.org/cabal/ if you need that. Sometimes, repeated installations and re-installations can result in a thoroughly unusable state of the Cabal package collection. If you get error messages that just don't make sense anymore, please refer to http://www.vex.net/~trebla/haskell/sicp.xhtml; among other useful things, it tells you how to wipe a package database without causing further destruction.