# bwa-0.7.17 **Repository Path**: bioinformatics-dev/bwa-0.7.17 ## Basic Information - **Project Name**: bwa-0.7.17 - **Description**: No description available - **Primary Language**: Unknown - **License**: Not specified - **Default Branch**: master - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2022-01-17 - **Last Updated**: 2022-01-17 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README [![Build Status](https://travis-ci.org/lh3/bwa.svg?branch=dev)](https://travis-ci.org/lh3/bwa) ## Getting started git clone https://github.com/lh3/bwa.git cd bwa; make ./bwa index ref.fa ./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz ./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz ## Introduction BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to a few megabases. BWA-MEM and BWA-SW share similar features such as the support of long reads and chimeric alignment, but BWA-MEM, which is the latest, is generally recommended as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads. For all the algorithms, BWA first needs to construct the FM-index for the reference genome (the **index** command). Alignment algorithms are invoked with different sub-commands: **aln/samse/sampe** for BWA-backtrack, **bwasw** for BWA-SW and **mem** for the BWA-MEM algorithm. ## Availability BWA is released under [GPLv3][1]. The latest source code is [freely available at github][2]. Released packages can [be downloaded][3] at SourceForge. After you acquire the source code, simply use `make` to compile and copy the single executable `bwa` to the destination you want. The only dependency required to build BWA is [zlib][14]. Since 0.7.11, precompiled binary for x86\_64-linux is available in [bwakit][17]. In addition to BWA, this self-consistent package also comes with bwa-associated and 3rd-party tools for proper BAM-to-FASTQ conversion, mapping to ALT contigs, adapter triming, duplicate marking, HLA typing and associated data files. ## Seeking help The detailed usage is described in the man page available together with the source code. You can use `man ./bwa.1` to view the man page in a terminal. The [HTML version][4] of the man page can be found at the [BWA website][5]. If you have questions about BWA, you may [sign up the mailing list][6] and then send the questions to [bio-bwa-help@sourceforge.net][7]. You may also ask questions in forums such as [BioStar][8] and [SEQanswers][9]. ## Citing BWA * Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. *Bioinformatics*, **25**, 1754-1760. [PMID: [19451168][10]]. (if you use the BWA-backtrack algorithm) * Li H. and Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. *Bioinformatics*, **26**, 589-595. [PMID: [20080505][11]]. (if you use the BWA-SW algorithm) * Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. [arXiv:1303.3997v2][12] [q-bio.GN]. (if you use the BWA-MEM algorithm or the **fastmap** command, or want to cite the whole BWA package) Please note that the last reference is a preprint hosted at [arXiv.org][13]. I do not have plan to submit it to a peer-reviewed journal in the near future. ## Frequently asked questions (FAQs) 1. [What types of data does BWA work with?](#type) 2. [Why does a read appear multiple times in the output SAM?](#multihit) 3. [Does BWA work on reference sequences longer than 4GB in total?](#4gb) 4. [Why can one read in a pair has high mapping quality but the other has zero?](#pe0) 5. [How can a BWA-backtrack alignment stands out of the end of a chromosome?](#endref) 6. [Does BWA work with ALT contigs in the GRCh38 release?](#altctg) 7. [Can I just run BWA-MEM against GRCh38+ALT without post-processing?](#postalt) #### 1. What types of data does BWA work with? BWA works with a variety types of DNA sequence data, though the optimal algorithm and setting may vary. The following list gives the recommended settings: * Illumina/454/IonTorrent single-end reads longer than ~70bp or assembly contigs up to a few megabases mapped to a closely related reference genome: bwa mem ref.fa reads.fq > aln.sam * Illumina single-end reads shorter than ~70bp: bwa aln ref.fa reads.fq > reads.sai; bwa samse ref.fa reads.sai reads.fq > aln-se.sam * Illumina/454/IonTorrent paired-end reads longer than ~70bp: bwa mem ref.fa read1.fq read2.fq > aln-pe.sam * Illumina paired-end reads shorter than ~70bp: bwa aln ref.fa read1.fq > read1.sai; bwa aln ref.fa read2.fq > read2.sai bwa sampe ref.fa read1.sai read2.sai read1.fq read2.fq > aln-pe.sam * PacBio subreads or Oxford Nanopore reads to a reference genome: bwa mem -x pacbio ref.fa reads.fq > aln.sam bwa mem -x ont2d ref.fa reads.fq > aln.sam BWA-MEM is recommended for query sequences longer than ~70bp for a variety of error rates (or sequence divergence). Generally, BWA-MEM is more tolerant with errors given longer query sequences as the chance of missing all seeds is small. As is shown above, with non-default settings, BWA-MEM works with Oxford Nanopore reads with a sequencing error rate over 20%. #### 2. Why does a read appear multiple times in the output SAM? BWA-SW and BWA-MEM perform local alignments. If there is a translocation, a gene fusion or a long deletion, a read bridging the break point may have two hits, occupying two lines in the SAM output. With the default setting of BWA-MEM, one and only one line is primary and is soft clipped; other lines are tagged with 0x800 SAM flag (supplementary alignment) and are hard clipped. #### 3. Does BWA work on reference sequences longer than 4GB in total? Yes. Since 0.6.x, all BWA algorithms work with a genome with total length over 4GB. However, individual chromosome should not be longer than 2GB. #### 4. Why can one read in a pair have a high mapping quality but the other has zero? This is correct. Mapping quality is assigned for individual read, not for a read pair. It is possible that one read can be mapped unambiguously, but its mate falls in a tandem repeat and thus its accurate position cannot be determined. #### 5. How can a BWA-backtrack alignment stand out of the end of a chromosome? Internally BWA concatenates all reference sequences into one long sequence. A read may be mapped to the junction of two adjacent reference sequences. In this case, BWA-backtrack will flag the read as unmapped (0x4), but you will see position, CIGAR and all the tags. A similar issue may occur to BWA-SW alignment as well. BWA-MEM does not have this problem. #### 6. Does BWA work with ALT contigs in the GRCh38 release? Yes, since 0.7.11, BWA-MEM officially supports mapping to GRCh38+ALT. BWA-backtrack and BWA-SW don't properly support ALT mapping as of now. Please see [README-alt.md][18] for details. Briefly, it is recommended to use [bwakit][17], the binary release of BWA, for generating the reference genome and for mapping. #### 7. Can I just run BWA-MEM against GRCh38+ALT without post-processing? If you are not interested in hits to ALT contigs, it is okay to run BWA-MEM without post-processing. The alignments produced this way are very close to alignments against GRCh38 without ALT contigs. Nonetheless, applying post-processing helps to reduce false mappings caused by reads from the diverged part of ALT contigs and also enables HLA typing. It is recommended to run the post-processing script. [1]: http://en.wikipedia.org/wiki/GNU_General_Public_License [2]: https://github.com/lh3/bwa [3]: http://sourceforge.net/projects/bio-bwa/files/ [4]: http://bio-bwa.sourceforge.net/bwa.shtml [5]: http://bio-bwa.sourceforge.net/ [6]: https://lists.sourceforge.net/lists/listinfo/bio-bwa-help [7]: mailto:bio-bwa-help@sourceforge.net [8]: http://biostars.org [9]: http://seqanswers.com/ [10]: http://www.ncbi.nlm.nih.gov/pubmed/19451168 [11]: http://www.ncbi.nlm.nih.gov/pubmed/20080505 [12]: http://arxiv.org/abs/1303.3997 [13]: http://arxiv.org/ [14]: http://zlib.net/ [15]: https://github.com/lh3/bwa/tree/mem [16]: ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/ [17]: http://sourceforge.net/projects/bio-bwa/files/bwakit/ [18]: https://github.com/lh3/bwa/blob/master/README-alt.md