Parallel BWA [pBWA] download

Parallel implementation of BWA (http://bio-bwa.sourceforge.net/) using the OpenMPI library.

Features

Parallel implementation of BWA's aln, sampe, and samse commands
More efficient multithreading than BWA for aln
Can combine parallelism and multithreading for aln
Future releases will see sampe and samse given multithreading options
Unfortunately, pBWA does not support gzipped input read files

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License

GNU General Public License version 3.0 (GPLv3), MIT License

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williamdanis Posted 2013-06-09

Easy for use.

2 users found this review helpful.
abynarain Posted 2013-02-26

Error when I try to install using make command: mpicc -g -m64 -O2 -DHAVE_PTHREAD -D_LARGEFILE64_SOURCE utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o pBWA -lm -lz -lpthread -Lbwt_gen -lbwtgen /usr/bin/ld: cannot find -lbwtgen collect2: ld returned 1 exit status make: *** [pBWA] Error 1
bioruan Posted 2012-07-16

Hi, how to install it? I run $ make in the folder and got these lines make[1]: Entering directory `/home/ruan/pkgs/pBWA' make[1]: Nothing to be done for `lib'. make[1]: Leaving directory `/home/ruan/pkgs/pBWA' make[1]: Entering directory `/home/ruan/pkgs/pBWA/bwt_gen' mpicc -c -g -Wall -m64 -O2 -DHAVE_PTHREAD -D_LARGEFILE64_SOURCE bwt_gen.c -o bwt_gen.o make[1]: mpicc: Command not found make[1]: *** [bwt_gen.o] Error 127 make[1]: Leaving directory `/home/ruan/pkgs/pBWA/bwt_gen' make: *** [lib-recur] Error 1

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Registered

2011-04-03

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