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updated README, a bit

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Heng Li 2014-10-14 23:46:59 -04:00
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@ -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)
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 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
* 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
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.