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Add KrakenUniq and Filtlong in documentation

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Sofia Stamouli 2022-10-11 12:36:48 +02:00 committed by GitHub
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@ -32,8 +32,8 @@ On release, automated continuous integration tests run the pipeline on a full-si
1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
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 filtering ([bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus))
- 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 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 ([BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/))
- Run merging
3. Performs taxonomic profiling using one or more of:
@ -44,7 +44,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
- [Centrifuge](https://ccb.jhu.edu/software/centrifuge/)
- [Kaiju](https://kaiju.binf.ku.dk/)
- [mOTUs](https://motu-tool.org/)
- [MetaMaps](https://github.com/DiltheyLab/MetaMaps)
- [KrakenUniq](https://github.com/fbreitwieser/krakenuniq)
4. Perform optional post-processing with:
- [bracken](https://ccb.jhu.edu/software/bracken/)
5. Standardises output tables