Parallel BWA [pBWA]

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Download pBWA_0.5.9-1.21009.zip
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Description

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

Parallel BWA [pBWA] Web Site

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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User Reviews

  • williamdanis
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    Easy for use.

    Posted 06/09/2013
  • abynarain
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    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

    Posted 02/26/2013
  • bioruan
    1 of 5 2 of 5 3 of 5 4 of 5 5 of 5

    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

    Posted 07/16/2012
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Additional Project Details

Registered

2011-04-03
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