zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

updated README, a bit

This commit is contained in:
Heng Li 2014-10-14 23:46:59 -04:00
parent 71277f0fea
commit c44357926f
1 changed files with 4 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
README.md
View File

@ -63,7 +63,6 @@ do not have plan to submit it to a peer-reviewed journal in the near future.
3. [Does BWA work on reference sequences longer than 4GB in total?](#4gb) 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) 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) 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 name="type"></a>1. What types of data does BWA work with? ####<a name="type"></a>1. What types of data does BWA work with?
@ -93,6 +92,10 @@ settings:
bwa mem -x pacbio ref.fa reads.fq > aln.sam bwa mem -x pacbio ref.fa reads.fq > aln.sam
* Oxford Nanopore reads to a reference genome:
bwa mem -x ont2d ref.fa reads.fq > aln.sam
BWA-MEM is recommended for query sequences longer than ~70bp for a variety of 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 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. errors given longer query sequences as the chance of missing all seeds is small.