Workflows

Created At
Go
101 Workflows visible to you, out of a total of 143

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

usegalaxy.org usegalaxy.eu usegalaxy.org.au usegalaxy.be

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 ...

Type: Galaxy

Creator: Finn Bacall

Submitter: Finn Bacall

BROAD Best Practices Somatic CNV Panel is used for creating a panel of normals (PON) given a set of normal samples.

Common Use Cases

For CNV discovery, the PON is created by running the initial coverage collection tools individually on a set of normal samples and combining the resulting copy ratio data using a dedicated PON creation tool [1]. This produces a binary file that can be used as a PON. It is very important to use normal samples that are as technically similar as possible to the ...

Type: Common Workflow Language

Creator: Kaushik Ghose

Submitter: Kaushik Ghose

Runs InterProScan on batches of sequences to retrieve functional annotations.

Type: Common Workflow Language

Creator: Maxim Scheremetjew

Submitter: Finn Bacall

Transcripts annotation workflow

Type: Common Workflow Language

Creators: None

Submitter: Finn Bacall

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' ...

Type: Nextflow

Creator: Olga Botvinnik

Submitter: Finn Bacall

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/ ...

Type: Nextflow

Creator: No author provided

Submitter: Finn Bacall

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. ...

Type: Nextflow

Creator: Phil Ewels

Submitter: Finn Bacall

Powered by
(v.1.12.0-master)
Copyright © 2008 - 2021 The University of Manchester and HITS gGmbH