bwa/bwa-0.7.17/README.md

12 BWA is a software package for mapping DNA sequences against a large reference
14 BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina
16 70bp to a few megabases. BWA-MEM and BWA-SW share similar features such as the
17 support of long reads and chimeric alignment, but BWA-MEM, which is the latest,
18 is generally recommended as it is faster and more accurate. BWA-MEM also has
19 better performance than BWA-backtrack for 70-100bp Illumina reads.
21 For all the algorithms, BWA first needs to construct the FM-index for the
23 different sub-commands: **aln/samse/sampe** for BWA-backtrack,
24 **bwasw** for BWA-SW and **mem** for the BWA-MEM algorithm.
28 BWA is released under [GPLv3][1]. The latest source code is [freely
32 dependency required to build BWA is [zlib][14].
35 In addition to BWA, this self-consistent package also comes with bwa-associated
43 [HTML version][4] of the man page can be found at the [BWA website][5]. If you
44 have questions about BWA, you may [sign up the mailing list][6] and then send
48 ## Citing BWA
52  [19451168][10]]. (if you use the BWA-backtrack algorithm)
56  [20080505][11]]. (if you use the BWA-SW algorithm)
59  with BWA-MEM. [arXiv:1303.3997v2][12] [q-bio.GN]. (if you use the BWA-MEM
60  algorithm or the **fastmap** command, or want to cite the whole BWA package)
67 1. [What types of data does BWA work with?](#type)
69 3. [Does BWA work on reference sequences longer than 4GB in total?](#4gb)
71 5. [How can a BWA-backtrack alignment stands out of the end of a chromosome?](#endref)
72 6. [Does BWA work with ALT contigs in the GRCh38 release?](#altctg)
73 7. [Can I just run BWA-MEM against GRCh38+ALT without post-processing?](#postalt)
75 #### <a name="type"></a>1. What types of data does BWA work with?
77 BWA works with a variety types of DNA sequence data, though the optimal
104 BWA-MEM is recommended for query sequences longer than ~70bp for a variety of
105 error rates (or sequence divergence). Generally, BWA-MEM is more tolerant with
107 As is shown above, with non-default settings, BWA-MEM works with Oxford Nanopore
112 BWA-SW and BWA-MEM perform local alignments. If there is a translocation, a gene
114 occupying two lines in the SAM output. With the default setting of BWA-MEM, one
118 #### <a name="4gb"></a>3. Does BWA work on reference sequences longer than 4GB in total?
120 Yes. Since 0.6.x, all BWA algorithms work with a genome with total length over
129 #### <a name="endref"></a>5. How can a BWA-backtrack alignment stand out of the end of a chromosome?
131 Internally BWA concatenates all reference sequences into one long sequence. A
133 case, BWA-backtrack will flag the read as unmapped (0x4), but you will see
134 position, CIGAR and all the tags. A similar issue may occur to BWA-SW alignment
135 as well. BWA-MEM does not have this problem.
137 #### <a name="altctg"></a>6. Does BWA work with ALT contigs in the GRCh38 release?
139 Yes, since 0.7.11, BWA-MEM officially supports mapping to GRCh38+ALT.
140 BWA-backtrack and BWA-SW don't properly support ALT mapping as of now. Please
142 [bwakit][17], the binary release of BWA, for generating the reference genome
145 #### <a name="postalt"></a>7. Can I just run BWA-MEM against GRCh38+ALT without post-processing?
147 If you are not interested in hits to ALT contigs, it is okay to run BWA-MEM