Workflows

Assembly of SARS-CoV-2 from pre-processed reads

Live Resources

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

What's the point?

Use a combination of Illumina and Oxford Nanopore reads to produce SARS-CoV-2 genome assembly.

Outline

We use Illumina and Oxford Nanopore reads that were pre-processed to remove human-derived sequences. We use two assembly tools: spades and unicycler. While spades is a tool fully dedicated to assembly, unicycler is a "wrapper" that combines multiple existing ...

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 ...

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 ...

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/ ...