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don't use bullets - they are hard to read

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Heng Li 2018-03-12 12:42:13 -04:00
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cookbook.md
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@ -16,40 +16,40 @@ curl -L https://github.com/lh3/minimap2/releases/download/v2.0/cookbook-data.tgz
## <a name="map-reads"></a>Mapping Genomic Reads ## <a name="map-reads"></a>Mapping Genomic Reads
* Map example E. coli PacBio reads (takes about 12 wall-clock seconds): ### Map PacBio reads
```sh ```sh
minimap2 -ax map-pb -t4 ecoli_ref.fa ecoli_p6_25x_canu.fa > mapped.sam minimap2 -ax map-pb -t4 ecoli_ref.fa ecoli_p6_25x_canu.fa > mapped.sam
``` ```
Alternatively, you can create a minimap2 index first and then map: Alternatively, you can create a minimap2 index first and then map:
```sh ```sh
minimap2 -x map-pb -d ecoli-pb.mmi ecoli_ref.fa # create an index minimap2 -x map-pb -d ecoli-pb.mmi ecoli_ref.fa # create an index
minimap2 -ax map-pb ecoli-pb.mmi ecoli_p6_25x_canu.fa > mapped.sam minimap2 -ax map-pb ecoli-pb.mmi ecoli_p6_25x_canu.fa > mapped.sam
``` ```
This will save you a couple of minutes when you map against the human genome. This will save you a couple of minutes when you map against the human genome.
**HOWEVER**, key algorithm parameters such as the k-mer length and window **HOWEVER**, key algorithm parameters such as the k-mer length and window
size can't be changed after indexing. Minimap2 will give you a warning if size can't be changed after indexing. Minimap2 will give you a warning if
parameters used in a pre-built index doesn't match parameters on the command parameters used in a pre-built index doesn't match parameters on the command
line. *Please always make sure you are using an intended pre-built index.* line. *Please always make sure you are using an intended pre-built index.*
* Map Illumina paired-end reads: ### Map Illumina paired-end reads:
```sh ```sh
minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq > mapped-sr.sam minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq > mapped-sr.sam
``` ```
* Evaluating mapping accuracy with simulated reads: ### Evaluating mapping accuracy with simulated reads:
```sh ```sh
minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq | paftools.js mapeval - minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq | paftools.js mapeval -
``` ```
The output is: The output is:
``` ```
Q 60 19712 0 0.000000000 19712 Q 60 19712 0 0.000000000 19712
Q 0 282 219 0.010953286 19994 Q 0 282 219 0.010953286 19994
U 6 U 6
``` ```
where a line starting with `Q` gives: where a line starting with `Q` gives:
1. Mapping quality (mapQ) threshold 1. Mapping quality (mapQ) threshold
2. Number of mapped reads between this threshold and the previous mapQ threshold. 2. Number of mapped reads between this threshold and the previous mapQ threshold.
3. Number of wrong mappings in the same mapQ interval 3. Number of wrong mappings in the same mapQ interval
4. Accumulative mapping error rate 4. Accumulative mapping error rate
5. Accumulative number of mappings 5. Accumulative number of mappings
A `U` line gives the number of unmapped reads (for SAM input only) A `U` line gives the number of unmapped reads (for SAM input only).