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Add samtools to README

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Sofia Stamouli 2022-11-03 16:52:01 +01:00 committed by GitHub
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@ -34,9 +34,10 @@ On release, automated continuous integration tests run the pipeline on a full-si
2. Performs optional read pre-processing 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)) - 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)) - 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 - 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/) - [Kraken2](https://ccb.jhu.edu/software/kraken2/)
- [MetaPhlAn3](https://huttenhower.sph.harvard.edu/metaphlan/) - [MetaPhlAn3](https://huttenhower.sph.harvard.edu/metaphlan/)
- [MALT](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/) - [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/) - [Kaiju](https://kaiju.binf.ku.dk/)
- [mOTUs](https://motu-tool.org/) - [mOTUs](https://motu-tool.org/)
- [KrakenUniq](https://github.com/fbreitwieser/krakenuniq) - [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/) - [bracken](https://ccb.jhu.edu/software/bracken/)
5. Standardises output tables 6. Standardises output tables
6. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) 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)) 7. Plotting Kraken2, Centrifuge, Kaiju and MALT results ([`Krona`](https://hpc.nih.gov/apps/kronatools.html))
## Quick Start ## Quick Start