jivebunny is a probilistic demultiplexer for double-indexed Illumina
sequencing runs. It is intended to both detect and remove contamination
with unexpected libraries, and to demultiplex while providing an easy to
understand quality measure.
For the time being, we have jivebunny, which operates on BAM files
(and is a bit slow), and bcl2bam, which converts BCL to BAM. Ideally,
both functions should be merged into one tool.
jivebunny 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, version 8.4.4 is recommended) and cabal-install (see http://haskell.org/cabal, version 2.4.0.0 is recommended),
cabal update(takes a while to download the current package list),git clone https://ustenzel@bitbucket.org/ustenzel/jivebunny.gitcabal install jivebunny/
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 more destruction.