Benchmarking: BWA 0.7.12 - Burrows-Wheeler Aligner
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- Download 0.7.12 from: wget 'http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.12.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbio-bwa%2F&ts=1424211953&use_mirror=switch'
[david@head-Boston bwa]$ tar jxvf bwa-0.7.12.tar.bz2
bwa-0.7.12/
bwa-0.7.12/bamlite.c
bwa-0.7.12/bamlite.h
bwa-0.7.12/bntseq.c
bwa-0.7.12/bntseq.h
bwa-0.7.12/bwa.1
bwa-0.7.12/bwa.c
bwa-0.7.12/bwa.h
bwa-0.7.12/bwakit/
bwa-0.7.12/bwamem.c
bwa-0.7.12/bwamem.h
bwa-0.7.12/bwamem_extra.c
bwa-0.7.12/bwamem_pair.c
bwa-0.7.12/bwape.c
bwa-0.7.12/bwase.c
bwa-0.7.12/bwase.h
bwa-0.7.12/bwaseqio.c
bwa-0.7.12/bwashm.c
bwa-0.7.12/bwt.c
bwa-0.7.12/bwt.h
bwa-0.7.12/bwt_gen.c
bwa-0.7.12/bwt_lite.c
bwa-0.7.12/bwt_lite.h
bwa-0.7.12/bwtaln.c
bwa-0.7.12/bwtaln.h
bwa-0.7.12/bwtgap.c
bwa-0.7.12/bwtgap.h
bwa-0.7.12/bwtindex.c
bwa-0.7.12/bwtsw2.h
bwa-0.7.12/bwtsw2_aux.c
bwa-0.7.12/bwtsw2_chain.c
bwa-0.7.12/bwtsw2_core.c
bwa-0.7.12/bwtsw2_main.c
bwa-0.7.12/bwtsw2_pair.c
bwa-0.7.12/ChangeLog
bwa-0.7.12/COPYING
bwa-0.7.12/example.c
bwa-0.7.12/fastmap.c
bwa-0.7.12/is.c
bwa-0.7.12/kbtree.h
bwa-0.7.12/khash.h
bwa-0.7.12/kopen.c
bwa-0.7.12/kseq.h
bwa-0.7.12/ksort.h
bwa-0.7.12/kstring.c
bwa-0.7.12/kstring.h
bwa-0.7.12/ksw.c
bwa-0.7.12/ksw.h
bwa-0.7.12/kthread.c
bwa-0.7.12/kvec.h
bwa-0.7.12/main.c
bwa-0.7.12/Makefile
bwa-0.7.12/malloc_wrap.c
bwa-0.7.12/malloc_wrap.h
bwa-0.7.12/NEWS.md
bwa-0.7.12/pemerge.c
bwa-0.7.12/QSufSort.c
bwa-0.7.12/QSufSort.h
bwa-0.7.12/qualfa2fq.pl
bwa-0.7.12/README-alt.md
bwa-0.7.12/README.md
bwa-0.7.12/utils.c
bwa-0.7.12/utils.h
bwa-0.7.12/xa2multi.pl
bwa-0.7.12/bwakit/bwa-postalt.js
bwa-0.7.12/bwakit/README.md
bwa-0.7.12/bwakit/run-bwamem
bwa-0.7.12/bwakit/run-gen-ref
bwa-0.7.12/bwakit/run-HLA
bwa-0.7.12/bwakit/typeHLA-selctg.js
bwa-0.7.12/bwakit/typeHLA.js
bwa-0.7.12/bwakit/typeHLA.sh
[david@head-Boston bwa]$ ls
bwa-0.7.12 bwa-0.7.12.tar.bz2
[david@head-Boston bwa]$ cd bwa-0.7.12
[david@head-Boston bwa-0.7.12]$ ls
bamlite.c bwa.h bwape.c bwtaln.h bwtindex.c bwtsw2.h fastmap.c ksort.h kvec.h pemerge.c utils.c
bamlite.h bwakit bwase.c bwt.c bwt_lite.c bwtsw2_main.c is.c kstring.c main.c QSufSort.c utils.h
bntseq.c bwamem.c bwase.h bwtgap.c bwt_lite.h bwtsw2_pair.c kbtree.h kstring.h Makefile QSufSort.h xa2multi.pl
bntseq.h bwamem_extra.c bwaseqio.c bwtgap.h bwtsw2_aux.c ChangeLog khash.h ksw.c malloc_wrap.c qualfa2fq.pl
bwa.1 bwamem.h bwashm.c bwt_gen.c bwtsw2_chain.c COPYING kopen.c ksw.h malloc_wrap.h README-alt.md
bwa.c bwamem_pair.c bwtaln.c bwt.h bwtsw2_core.c example.c kseq.h kthread.c NEWS.md README.md
[david@head-Boston bwa-0.7.12]$ make
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o
gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o
gcc -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
[david@head-Boston bwa-0.7.12]$ ls
bamlite.c bwa.h bwa.o bwashm.o bwt_gen.o bwtsw2_aux.o bwtsw2_pair.o khash.h ksw.h malloc_wrap.c qualfa2fq.pl
bamlite.h bwakit bwape.c bwtaln.c bwt.h bwtsw2_chain.c ChangeLog kopen.c ksw.o malloc_wrap.h README-alt.md
bamlite.o bwamem.c bwape.o bwtaln.h bwtindex.c bwtsw2_chain.o COPYING kopen.o kthread.c malloc_wrap.o README.md
bntseq.c bwamem_extra.c bwase.c bwtaln.o bwtindex.o bwtsw2_core.c example.c kseq.h kthread.o NEWS.md utils.c
bntseq.h bwamem_extra.o bwase.h bwt.c bwt_lite.c bwtsw2_core.o fastmap.c ksort.h kvec.h pemerge.c utils.h
bntseq.o bwamem.h bwase.o bwtgap.c bwt_lite.h bwtsw2.h fastmap.o kstring.c libbwa.a pemerge.o utils.o
bwa bwamem.o bwaseqio.c bwtgap.h bwt_lite.o bwtsw2_main.c is.c kstring.h main.c QSufSort.c xa2multi.pl
bwa.1 bwamem_pair.c bwaseqio.o bwtgap.o bwt.o bwtsw2_main.o is.o kstring.o main.o QSufSort.h
bwa.c bwamem_pair.o bwashm.c bwt_gen.c bwtsw2_aux.c bwtsw2_pair.c kbtree.h ksw.c Makefile QSufSort.o
[david@head-Boston bwa-0.7.12]$ ./bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.12-r1039
Contact: Heng Li <lh3@sanger.ac.uk>
Usage: bwa <command> [options]
Command: index index sequences in the FASTA format
mem BWA-MEM algorithm
fastmap identify super-maximal exact matches
pemerge merge overlapping paired ends (EXPERIMENTAL)
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries
shm manage indices in shared memory
fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generating BWT
bwtupdate update .bwt to the new format
bwt2sa generate SA from BWT and Occ
Note: To use BWA, you need to first index the genome with `bwa index'.
There are three alignment algorithms in BWA: `mem', `bwasw', and
`aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
first. Please `man ./bwa.1' for the manual.