From 024b6836717c8fcd6efd9582d56429fba18797f8 Mon Sep 17 00:00:00 2001 From: sofstam Date: Tue, 17 Jan 2023 15:38:56 +0100 Subject: [PATCH] Update output and usage --- docs/output.md | 18 +++++++++++++++++- docs/usage.md | 1 - 2 files changed, 17 insertions(+), 2 deletions(-) diff --git a/docs/output.md b/docs/output.md index ca15138..3257860 100644 --- a/docs/output.md +++ b/docs/output.md @@ -58,7 +58,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ### fastp -fastp can automatically detect adapter sequences for Illumina data. +[fastp](https://github.com/OpenGene/fastp) is a FASTQ pre-processing tool for quality control, trimmming of adapters, quality filtering and other features. + +It is used in nf-core/taxprofiler for adapter trimming of short-reads.
Output files @@ -141,6 +143,8 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t ### Filtlong +[Filtlong](https://github.com/rrwick/Filtlong) is a quality filtering tool for long reads. +
Output files @@ -172,6 +176,10 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t ### minimap2 +[minimap2](https://github.com/lh3/minimap2) is an alignment tool suited to mapping long reads to reference sequences. + +It is used with nf-core/taxprofiler to allow removal of 'host' (e.g. human) or other possible contaminant reads from the FASTQ files prior to taxonomic classification/profiling. +
Output files @@ -182,6 +190,8 @@ Note that the FASTQ file(s) may _not_ always be the 'final' reads that go into t ### Samtools stats +[Samtools stats](http://www.htslib.org/doc/samtools-stats.html) collects statistics from an alignment file and outputs in a text format. +
Output files @@ -254,6 +264,8 @@ You will only receive the FASTQs and `*classifiedreads.txt` file if you supply ` ### Centrifuge +[Centrifuge](https://github.com/DaehwanKimLab/centrifuge) is a taxonomic sequence classifier that uses a Burrows-Wheeler transform and Ferragina-Manzina index for storing and mapping sequences. +
Output files @@ -279,6 +291,8 @@ You will only receive the FASTQs and `*classifiedreads.txt` file if you supply ` ### DIAMOND +[DIAMOND](https://github.com/bbuchfink/diamond) is a sequence aligner for translated DNA searches or protein sequences against a protein reference database such as NR. It is a replacement for the NCBI BLAST software tools.It has many key features and it is used as taxonomic classifier in nf-core/taxprofiler. +
Output files @@ -328,6 +342,8 @@ You will only recieve the `.sam` and `.megan` files if you supply `--malt_save_r The main taxonomic profiling file from MetaPhlAn3 is the `*_profile.txt` file. This provides the abundance estimates from MetaPhlAn3 however does not include raw counts by default. ### mOTUs +[mOTUS](https://github.com/motu-tool/mOTUs) maps reads to a unique marker specific database and estimates the relative abundance of known and unknown species. +
Output files diff --git a/docs/usage.md b/docs/usage.md index 9539a5a..0edd065 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -631,7 +631,6 @@ krakenuniq-build --db --kmer-len 31 Please see the [KrakenUniq documentation](https://github.com/fbreitwieser/krakenuniq#database-building) for more information. -```` #### MALT custom database