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clarify CLR when necessary

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Heng Li 2021-05-01 15:56:33 -04:00
parent 817cb81cb0
commit f7dc5799c5
1 changed files with 4 additions and 4 deletions
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README.md
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@ -12,7 +12,7 @@ cd minimap2 && make
./minimap2 -x map-ont -d MT-human-ont.mmi test/MT-human.fa ./minimap2 -x map-ont -d MT-human-ont.mmi test/MT-human.fa
./minimap2 -a MT-human-ont.mmi test/MT-orang.fa > test.sam ./minimap2 -a MT-human-ont.mmi test/MT-orang.fa > test.sam
# use presets (no test data) # use presets (no test data)
./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio genomic reads ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio CLR genomic reads
./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads
./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads ./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads
./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam # short genomic paired-end reads ./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam # short genomic paired-end reads
@ -139,13 +139,13 @@ parameters at the same time. The default setting is the same as `map-ont`.
#### <a name="map-long-genomic"></a>Map long noisy genomic reads #### <a name="map-long-genomic"></a>Map long noisy genomic reads
```sh ```sh
minimap2 -ax map-pb ref.fa pacbio-reads.fq > aln.sam # for PacBio subreads minimap2 -ax map-pb ref.fa pacbio-reads.fq > aln.sam # for PacBio CLR reads
minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam # for Oxford Nanopore reads minimap2 -ax map-ont ref.fa ont-reads.fq > aln.sam # for Oxford Nanopore reads
``` ```
The difference between `map-pb` and `map-ont` is that `map-pb` uses The difference between `map-pb` and `map-ont` is that `map-pb` uses
homopolymer-compressed (HPC) minimizers as seeds, while `map-ont` uses ordinary homopolymer-compressed (HPC) minimizers as seeds, while `map-ont` uses ordinary
minimizers as seeds. Emperical evaluation suggests HPC minimizers improve minimizers as seeds. Emperical evaluation suggests HPC minimizers improve
performance and sensitivity when aligning PacBio reads, but hurt when aligning performance and sensitivity when aligning PacBio CLR reads, but hurt when aligning
Nanopore reads. Nanopore reads.
#### <a name="map-long-splice"></a>Map long mRNA/cDNA reads #### <a name="map-long-splice"></a>Map long mRNA/cDNA reads
@ -206,7 +206,7 @@ strand field. In this case, each line indicates an oriented junction.
#### <a name="long-overlap"></a>Find overlaps between long reads #### <a name="long-overlap"></a>Find overlaps between long reads
```sh ```sh
minimap2 -x ava-pb reads.fq reads.fq > ovlp.paf # PacBio read overlap minimap2 -x ava-pb reads.fq reads.fq > ovlp.paf # PacBio CLR read overlap
minimap2 -x ava-ont reads.fq reads.fq > ovlp.paf # Oxford Nanopore read overlap minimap2 -x ava-ont reads.fq reads.fq > ovlp.paf # Oxford Nanopore read overlap
``` ```
Similarly, `ava-pb` uses HPC minimizers while `ava-ont` uses ordinary Similarly, `ava-pb` uses HPC minimizers while `ava-ont` uses ordinary