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updated pbsim to pbsim2

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Heng Li 2021-07-17 18:18:26 -04:00
parent 5f449c5cae
commit 52fafe0fed
1 changed files with 4 additions and 4 deletions
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cookbook.md
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@ -80,12 +80,12 @@ where a `U`-line gives the number of unmapped reads (for SAM input only); a
5. Accumulative number of mappings 5. Accumulative number of mappings
For `paftools.js mapeval` to work, you need to encode the true read positions For `paftools.js mapeval` to work, you need to encode the true read positions
in read names in the right format. For [PBSIM][pbsim] and [mason2][mason2], we in read names in the right format. For [pbsim2][pbsim] and [mason2][mason2], we
provide scripts to generate the right format. Simulated reads in this cookbook provide scripts to generate the right format. Simulated reads in this cookbook
were created with the following command lines: were created with the following command lines:
```sh ```sh
# in PBSIM source code directory: # in the pbsim2 source code directory:
src/pbsim ../ecoli_ref.fa --depth 1 --sample-fastq sample/sample.fastq src/pbsim --depth 1 --length-min 5000 --length-mean 20000 --accuracy-mean 0.95 --hmm_model data/R94.model ../ecoli_ref.fa
paftools.js pbsim2fq ../ecoli_ref.fa.fai sd_0001.maf > ../ecoli_pbsim.fa paftools.js pbsim2fq ../ecoli_ref.fa.fai sd_0001.maf > ../ecoli_pbsim.fa
# mason2 simulation # mason2 simulation
@ -237,7 +237,7 @@ with `-x ava-pb` (99% vs 93% with `-x ava-ont`).
[pbsim]: https://github.com/pfaucon/PBSIM-PacBio-Simulator [pbsim]: https://github.com/yukiteruono/pbsim2
[mason2]: https://github.com/seqan/seqan/tree/master/apps/mason2 [mason2]: https://github.com/seqan/seqan/tree/master/apps/mason2
[paf]: https://github.com/lh3/miniasm/blob/master/PAF.md [paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
[v2.10]: https://github.com/lh3/minimap2/releases/tag/v2.10 [v2.10]: https://github.com/lh3/minimap2/releases/tag/v2.10