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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: * 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 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: * PacBio subreads to a reference genome:
bwa mem -x pacbio ref.fa reads.fq > aln.sam 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 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.