BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.

Features

  • Support Illumina, SOLiD, 454, Sanger reads, PacBio reads and assembly contigs
  • Gapped alignment and paired-end mapping
  • Accurate, fast and lightweight

Project Activity

See All Activity >

Categories

Bio-Informatics

License

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

Follow Burrows-Wheeler Aligner

Burrows-Wheeler Aligner Web Site

Other Useful Business Software
Migrate to innovate with Red Hat Enterprise Linux on Azure Icon
Migrate to innovate with Red Hat Enterprise Linux on Azure

Streamline your IT modernization journey with a holistic environment running Red Hat Enterprise Linux on Azure.

With Red Hat Enterprise Linux on Azure, businesses can confidently modernize their IT environment, knowing they don’t have to compromise on security, scalability, reliability, and ease of management. Securely accelerate innovation and unlock a competitive edge with enterprise-grade modern cloud infrastructure.
Rate This Project
Login To Rate This Project

User Ratings

★★★★★
★★★★
★★★
★★
5
0
1
0
0
ease 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 4 / 5
features 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 4 / 5
design 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 4 / 5
support 1 of 5 2 of 5 3 of 5 4 of 5 5 of 5 3 / 5

User Reviews

  • Excellent software - essential for many genomics applications.
  • Great software, thank you.
    1 user found this review helpful.
  • Error with make in the latest version. angelinadaniel@ubuntu:/media/angelinadaniel/linux/bwa-0.7.3a$ make gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD ksw.c -o ksw.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o bwt.c: In function ‘bwt_restore_bwt’: bwt.c:408:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:409:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:410:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c: In function ‘bwt_restore_sa’: bwt.c:382:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:384:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:385:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:386:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt.c:393:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o bntseq.c: In function ‘bns_restore_core’: bntseq.c:98:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:106:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:114:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:123:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] bntseq.c:129:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwa.c -o bwa.o bwa.c: In function ‘bwa_idx_load’: bwa.c:261:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwamem.c -o bwamem.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.o ar -csru libbwa.a utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o bwt_gen.c: In function ‘BWTIncBuildRelativeRank’: bwt_gen.c:873:10: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable] bwt_gen.c: In function ‘BWTIncMergeBwt’: bwt_gen.c:947:15: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable] bwt_gen.c: In function ‘BWTIncConstructFromPacked’: bwt_gen.c:1452:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt_gen.c:1468:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwt_gen.c:1483:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o bwase.c: In function ‘bwa_sai2sam_se_core’: bwase.c:516:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwase.c:530:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwase.c:535:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwase.c: In function ‘bwa_refine_gapped’: bwase.c:309:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o bwtindex.c: In function ‘bwt_pac2bwt’: bwtindex.c:73:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwtindex.c: In function ‘bwa_seq_len’: bwtindex.c:52:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o bwape.c: In function ‘bwa_sai2sam_pe_core’: bwape.c:642:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c:645:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c:653:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c: In function ‘bwa_paired_sw’: bwape.c:497:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c: In function ‘bwa_cal_pac_pos_pe’: bwape.c:278:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] bwape.c:282:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD kopen.c -o kopen.o kopen.c: In function ‘kopen’: kopen.c:265:8: warning: ignoring return value of ‘pipe’, declared with attribute warn_unused_result [-Wunused-result] kopen.c: In function ‘http_open’: kopen.c:93:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] kopen.c: In function ‘kftp_send_cmd’: kopen.c:146:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD pemerge.c -o pemerge.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o bwtsw2_aux.c: In function ‘bsw2_aln’: bwtsw2_aux.c:738:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD fastmap.c -o fastmap.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o gcc -g -Wall -O2 -DHAVE_PTHREAD QSufSort.o bwt_gen.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 gcc -c -g -Wall -O2 -DHAVE_PTHREAD example.c -o example.o gcc -g -Wall -O2 -DHAVE_PTHREAD example.o -o bwamem-lite -L. -lbwa -lm -lz -lpthread
    1 user found this review helpful.
  • HI, I downloaded the latest bwa (already been using bwa ). I tried to do 'make' to install but get an error, In file included from bwtaln.h:6, from bwaseqio.c:4: bwt.h:63: error: expected specifier-qualifier-list before âsize_tâ make: *** [bwaseqio.o] Error 1 Please can you help me here. I know this is a reviews page, but cannot find a way to post the message on any forum. Thanks.
  • Only consider BWA version 0.6.2 as the latest sufficiently tested and stable version. That said, this is a very good application for aligning short sequencing reads.
Read more reviews >

Additional Project Details

Operating Systems

Linux, BSD

Languages

English

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

C

Related Categories

C Bio-Informatics Software

Registered

2009-09-01