Workflows
What is a Workflow?Filters
Preprocessing of raw SARS-CoV-2 reads
The raw reads available so far are generated from bronchoalveolar lavage fluid (BALF) and are metagenomic in nature: they contain human reads, reads from potential bacterial co-infections as well as true COVID-19 reads.
Live Resources
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What's the point?
Assess quality of reads, remove adapters and remove reads mapping to human genome.
The outline
Illumina and Oxford nanopore reads are pulled from the ...
Runs InterProScan on batches of sequences to retrieve functional annotations.
Transcripts annotation workflow
nf-kmer-similarity
This is a Nextflow workflow for running k-mer similarity
Usage
With a samples.csv file:
nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ --samples samples.csv
With R1, R2 read pairs:
nextflow run czbiohub/nf-kmer-similarity --outdir s3://olgabot-maca/nf-kmer-similarity/ \ --read_pairs 's3://olgabot-maca/sra/homo_sapiens/smartseq2_quartzseq/{R1,R2}.fastq.gz,s3://olgabot-maca/sra/danio_rerio/smart-seq/whole_kidney_marrow_prjna393431/*{1,2}.fastq.gz' ...
Assembly, binning and annotation of metagenomes.
Introduction
This pipeline is for assembly, binning and annotation of metagenomes. It supports both short and long reads, quality trims the reads and adapters with https://github.com/OpenGene/fastp and https://github.com/rrwick/Porechop and performs basic QC with https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
The pipeline then:
assigns taxonomy to reads using https://ccb.jhu.edu/software/centrifuge/ and/or https://ccb.jhu.edu/software/kraken2/ ...
Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community..
The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. ...
Identify and quantify peptides from mass spectrometry raw data
Introduction
nfcore/mhcquant is a bioinformatics analysis pipeline used for quantitative processing of data dependant (DDA) peptidomics data.
It was specifically designed to analyse immunopeptidomics data, which deals with the analysis of affinity purified, unspecifically cleaved peptides that have recently been discussed intensively in the context of cancer vaccines.
The workflow is based on the OpenMS C++ framework for computational ...