From 52fafe0fed69ee2f3ef62080c67b4e5926e35a77 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 17 Jul 2021 18:18:26 -0400 Subject: [PATCH] updated pbsim to pbsim2 --- cookbook.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/cookbook.md b/cookbook.md index 8ff2bd0..8df1e28 100644 --- a/cookbook.md +++ b/cookbook.md @@ -80,12 +80,12 @@ where a `U`-line gives the number of unmapped reads (for SAM input only); a 5. Accumulative number of mappings 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 were created with the following command lines: ```sh -# in PBSIM source code directory: -src/pbsim ../ecoli_ref.fa --depth 1 --sample-fastq sample/sample.fastq +# in the pbsim2 source code directory: +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 # 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 [paf]: https://github.com/lh3/miniasm/blob/master/PAF.md [v2.10]: https://github.com/lh3/minimap2/releases/tag/v2.10