From 79dd3930bb0b714c99da55cb1c320c05295518f1 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Thu, 3 Nov 2022 16:52:01 +0100 Subject: [PATCH] Add samtools to README --- README.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 3f0a840..94ede1e 100644 --- a/README.md +++ b/README.md @@ -34,9 +34,10 @@ On release, automated continuous integration tests run the pipeline on a full-si 2. Performs optional read pre-processing - Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop)) - Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong)) - - Host read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2)) + - Host-read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2)) - Run merging -3. Performs taxonomic profiling using one or more of: +3. Supports statistics for host-read removal ([Samtools](http://www.htslib.org/)) +4. Performs taxonomic profiling using one or more of: - [Kraken2](https://ccb.jhu.edu/software/kraken2/) - [MetaPhlAn3](https://huttenhower.sph.harvard.edu/metaphlan/) - [MALT](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/) @@ -45,10 +46,10 @@ On release, automated continuous integration tests run the pipeline on a full-si - [Kaiju](https://kaiju.binf.ku.dk/) - [mOTUs](https://motu-tool.org/) - [KrakenUniq](https://github.com/fbreitwieser/krakenuniq) -4. Perform optional post-processing with: +5. Perform optional post-processing with: - [bracken](https://ccb.jhu.edu/software/bracken/) -5. Standardises output tables -6. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +6. Standardises output tables +7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) 7. Plotting Kraken2, Centrifuge, Kaiju and MALT results ([`Krona`](https://hpc.nih.gov/apps/kronatools.html)) ## Quick Start