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Removed PacBio read-to-read instruction

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Heng Li 2014-09-15 23:59:35 -04:00
parent d013ea94b0
commit 43ce69104d
1 changed files with 1 additions and 5 deletions
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README.md
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@ -87,16 +87,12 @@ settings:
* 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
bwa samsp ref.fa read1.sai read2.sai read1.fq read2.fq > aln-pe.sam
* PacBio subreads to a reference genome:
bwa mem -x pacbio ref.fa reads.fq > aln.sam
* PacBio subreads to themselves (the output is not SAM):
bwa mem -x pbread reads.fq reads.fq > overlap.pas
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.