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updated README

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Heng Li 2014-05-14 14:32:09 -04:00
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README.md
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###Introduction
BWA is a software package for mapping low-divergent sequences against a large
reference genome, such as the human genome. It consists of three algorithms:
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 1Mbp. 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.
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
@ -26,10 +25,10 @@ different sub-commands: **aln/samse/sampe** for BWA-backtrack,
###Availability
BWA is released under [GPLv3][1]. The latest souce code is [freely
available][2] at github. Released packages can [be downloaded][3] at
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 of BWA is [zlib][14].
dependency required to build BWA is [zlib][14].
###Seeking helps
@ -59,21 +58,37 @@ do not have plan to submit it to a peer-reviewed journal in the near future.
###Frequently asked questions (FAQs)
####What types of data does BWA work with?
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. [How to map sequences to GRCh38 with ALT contigs?](#h38)
####<a href="type"></a>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:
contigs up to a few megabases mapped to a close related reference genome:
bwa mem ref.fa reads.fq > aln.sam
* Illumina single-end reads no longer 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 no longer than ~70bp:
bwa aln ref.fa read1.fq > read1.sai; bwa aln ref.fa read2.fq > read2.sai
bwa samse ref.fa reads.sai reads.fq > aln-pe.sam
* PacBio subreads to a reference genome:
bwa mem -x pacbio ref.fa reads.fq > aln.sam
@ -82,24 +97,44 @@ settings:
bwa mem -x pbread reads.fq reads.fq > overlap.pas
* Illumina single-end reads no longer than ~70bp:
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 PacBio subreads
with a sequencing error rate as high as ~15%.
bwa aln ref.fa reads.fq > reads.sai; bwa samse ref.fa reads.sai reads.fq > aln-se.sam
####<a href="multihit"></a>2. Why does a read appear multiple times in the output SAM?
* Illumina paired-end reads no longer than ~70bp:
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.
bwa aln ref.fa read1.fq > read1.sai; bwa aln ref.fa read2.fq > read2.sai
bwa samse ref.fa reads.sai reads.fq > aln-pe.sam
####<a href="4gb"></a>3. Does BWA work on reference sequences longer than 4GB in total?
####Why does a read appear multiple times in the output SAM?
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.
BWA-SW and BWA-MEM perform local alignments.
####<a href="pe0"></a>4. Why can one read in a pair has high mapping quality but the other has zero?
####How to map sequences to GRCh38 with ALT contigs?
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.
####<a href="endref"></a>5. How can a BWA-backtrack alignment stands 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.
####<a href="h38"></a>6. How to map sequences to GRCh38 with ALT contigs?
BWA-backtrack and BWA-MEM partially support mapping to a reference containing
ALT contigs that represent alternative alleles highly divergent from the
reference genome.
reference genome.
# download the K8 executable required by bwa-helper.js
wget http://sourceforge.net/projects/lh3/files/k8/k8-0.2.1.tar.bz2/download