From c6710db7a9f1c82cd8ab4d4a863b61ae97c5edd7 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 20 Dec 2022 15:42:41 +0100 Subject: [PATCH] Apply review suggestion Co-authored-by: James A. Fellows Yates --- docs/output.md | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/docs/output.md b/docs/output.md index c4b04fd..372248a 100644 --- a/docs/output.md +++ b/docs/output.md @@ -99,15 +99,23 @@ Note that the FASTQ files may _not_ always be the 'final' reads that go into tax ### BBDuk +[BBDuk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/) stands for Decontamination Using Kmers. BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single high-performance tool. + +It is used in nf-core/taxprofiler for complexity filtering using different algorithms. This means that it will remove reads with low sequence diversity (e.g. mono- or dinucleotide repeats). +
Output files -- `bbduk` - - `.bbduk.log` - - `.fastq.gz` +- `bbduk/` + - `.bbduk.log`: log file containing filtering statistics + - `.fastq.gz`: resulting FASTQ file without low-complexity reads
+By default nf-core/taxprofiler will only provide the `.log` file if BBDuk is selected as the complexity filtering tool. You will only find the complexity filtered reads in your results directory if you provide ` --save_complexityfiltered_reads` . + +Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into taxprofiling, if you also run other steps such as host removal, run merging etc.. + ### PRINSEQ++