From 02517733aa2227d1bc6f4decdb607918de047b2d Mon Sep 17 00:00:00 2001 From: Lauri Mesilaakso Date: Fri, 6 May 2022 10:40:59 +0200 Subject: [PATCH] Update docs/usage.md Co-authored-by: James A. Fellows Yates --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 1143da3..4aa1d09 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -197,7 +197,7 @@ Similarly to complexity filtering, host-removal can be useful for runtime optimi nf-core/taxprofiler currently offers host-removal via alignment against a reference genome with Bowtie2, and the use of the unaligned reads for downstream profiling. -You can supply your reference genome in FASTA format with `--hostremoval_reference`. You can also optionally supply a directory containing pre-indexed Bowtie2 index files with `--shortread_hostremoval_index`, however nf-core/taxprofiler will generate this for you if necessary. Pre-supplying the directory of index files can greatly speed up the process, and these can be re-used. +You can supply your reference genome in FASTA format with `--hostremoval_reference`. You can also optionally supply a directory containing pre-indexed Bowtie2 index files with `--shortread_hostremoval_index` or `--longread_hostremoval_index`, however nf-core/taxprofiler will generate this for you if necessary. Pre-supplying the directory of index files can greatly speed up the process, and these can be re-used. > 💡 If you have multiple taxa or sequences you wish to remove (e.g., the host genome and then also PhiX - common quality-control reagent during sequencing) you can simply concatenate the FASTAs of each taxa or sequences into a single reference file.