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Merge pull request #142 from genomic-medicine-sweden/update_readme

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Add KrakenUniq and Filtlong in documentation
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Sofia Stamouli 2022-10-12 11:38:01 +02:00 committed by GitHub
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README.md
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@ -32,9 +32,9 @@ 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/)) 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
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 filtering ([bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus)) - 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 ([BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/)) - 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. Performs taxonomic profiling using one or more of:
- [Kraken2](https://ccb.jhu.edu/software/kraken2/) - [Kraken2](https://ccb.jhu.edu/software/kraken2/)
@ -44,15 +44,16 @@ On release, automated continuous integration tests run the pipeline on a full-si
- [Centrifuge](https://ccb.jhu.edu/software/centrifuge/) - [Centrifuge](https://ccb.jhu.edu/software/centrifuge/)
- [Kaiju](https://kaiju.binf.ku.dk/) - [Kaiju](https://kaiju.binf.ku.dk/)
- [mOTUs](https://motu-tool.org/) - [mOTUs](https://motu-tool.org/)
- [MetaMaps](https://github.com/DiltheyLab/MetaMaps) - [KrakenUniq](https://github.com/fbreitwieser/krakenuniq)
4. Perform optional post-processing with: 4. Perform optional post-processing with:
- [bracken](https://ccb.jhu.edu/software/bracken/) - [bracken](https://ccb.jhu.edu/software/bracken/)
5. Standardises output tables 5. Standardises output tables
6. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) 6. 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 ## Quick Start
1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`) 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`).
2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
@ -87,7 +88,7 @@ nf-core/taxprofiler was originally written by nf-core community.
We thank the following people for their extensive assistance in the development of this pipeline: We thank the following people for their extensive assistance in the development of this pipeline:
[James A. Fellows Yates](https://github.com/jfy133), [Moritz Beber](https://github.com/Midnighter), [Lauri Mesilaakso](https://github.com/ljmesi), [Sofia Stamouli](https://github.com/sofsam), [Maxime Borry](https://github.com/maxibor). [James A. Fellows Yates](https://github.com/jfy133), [Moritz Beber](https://github.com/Midnighter), [Lauri Mesilaakso](https://github.com/ljmesi), [Sofia Stamouli](https://github.com/sofsam), [Maxime Borry](https://github.com/maxibor),[Thomas A. Christensen II](https://github.com/MillironX), [Jianhong Ou](https://github.com/jianhong), [Rafal Stepien](https://github.com/rafalstepien), [Mahwash Jamy](https://github.com/mjamy).
## Contributions and Support ## Contributions and Support

1
docs/usage.md
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@ -47,6 +47,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th
A final samplesheet file consisting of both single- and paired-end data, as well as long-read FASTA files may look something like the one below. This is for 6 samples, where `2612` has been sequenced twice. A final samplesheet file consisting of both single- and paired-end data, as well as long-read FASTA files may look something like the one below. This is for 6 samples, where `2612` has been sequenced twice.
```console ```console
sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
2611,ERR5766174,ILLUMINA,,,/<path>/<to>/fasta/ERX5474930_ERR5766174_1.fa.gz 2611,ERR5766174,ILLUMINA,,,/<path>/<to>/fasta/ERX5474930_ERR5766174_1.fa.gz
2612,ERR5766176,ILLUMINA,/<path>/<to>/fastq/ERX5474932_ERR5766176_1.fastq.gz,/<path>/<to>/fastq/ERX5474932_ERR5766176_2.fastq.gz, 2612,ERR5766176,ILLUMINA,/<path>/<to>/fastq/ERX5474932_ERR5766176_1.fastq.gz,/<path>/<to>/fastq/ERX5474932_ERR5766176_2.fastq.gz,
2612,ERR5766180,ILLUMINA,/<path>/<to>/fastq/ERX5474936_ERR5766180_1.fastq.gz,, 2612,ERR5766180,ILLUMINA,/<path>/<to>/fastq/ERX5474936_ERR5766180_1.fastq.gz,,