From fcb189c8f39a66b6864a30153bd1391e4ebea58b Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Thu, 14 Mar 2024 11:06:46 +0100 Subject: [PATCH] improve fasta command title --- docs/user/writeFasta.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/user/writeFasta.md b/docs/user/writeFasta.md index ba7db52d..ac1ece26 100644 --- a/docs/user/writeFasta.md +++ b/docs/user/writeFasta.md @@ -1,20 +1,20 @@ -# Fasta +# Write pangenome sequences -This command can be used to write fasta sequences of the pangenome or specific parts of the pangenome. +The `fasta` command can be used to write sequences of the pangenome or specific parts of the pangenome in FASTA format. Most options require a partition. Available partitions are: -* 'all' for the entire pangenome. -* 'Persistent' for persistent families -* 'Shell' for shell genes or families -* 'Cloud' for cloud genes or families -* 'rgp' for genes or families found in RGPs -* 'core' for core genes or families -* 'softcore' for softcore genes or families - -When using the 'softcore' filter, the '--soft_core' option can be used to modify the threshold used to determine what is part of the softcore. It is set to 0.95 by default. +* `all` for the entire pangenome. +* `Persistent` for persistent families +* `Shell` for shell genes or families +* `Cloud` for cloud genes or families +* `rgp` for genes or families found in RGPs +* `core` for core genes or families +* `softcore` for softcore genes or families + +When using the `softcore` filter, the `--soft_core` option can be used to modify the threshold used to determine what is part of the softcore. It is set to 0.95 by default. ## Genes