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566 Workflows visible to you, out of a total of 671
Snakemake implementation of the Isoseq3.3 pipeline
Stable

Snakemake workflow: Isoseq3.3

Snakemake

This workflow implements the PacBio Isoseq v3.3.0 pipeline.

Note: Currently this workflow is limited to non-multiplexed samples.

Authors

  • Terry Bertozzi

Usage

If you use this workflow in a paper, don't forget to cite the URL of this (original) repository and, if available, its DOI (see above).

Step 1: Obtain a copy of this workflow

  1. Create ...

Type: Snakemake

Creator: Terry Bertozzi

Submitter: Terry Bertozzi

SomaticShortV-nf
Work-in-progress
No description specified

Type: Nextflow

Creators: Nandan Deshpande, Georgie Samaha

Submitter: Nandan Deshpande

PacBio HiFi genome assembly using hifiasm v2.1
Stable

Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.

Type: Galaxy

Creators: Gareth Price, Katherine Farquharson

Submitter: Johan Gustafsson

PacBio HiFi genome assembly using hifiasm v2.1
Stable

Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.

Type: Galaxy

Creators: Gareth Price, Katherine Farquharson

Submitter: Johan Gustafsson

PacBio HiFi genome assembly using hifiasm v2.1

Assembly, visualisation and quality control workflow for high fidelity reads built from circular consensus sequence (PacBio HiFi) data.

Type: Galaxy

Creators: Gareth Price, Katherine Farquharson

Submitter: Johan Gustafsson

SSQuAWK4.0.2

SARS-CoV-2 Sequence Quality Assurance Workflow Kontraption, version 4.0.2

Type: Galaxy

Creators: None

Submitter: Stian Soiland-Reyes

atacseq/main

This workflow take as input a collection of paired fastq. It will remove bad quality and adapters with cutadapt. Map with Bowtie2 end-to-end. Will remove reads on MT and unconcordant pairs and pairs with mapping quality below 30 and PCR duplicates. Will compute the pile-up on 5' +- 100bp. Will call peaks and count the number of reads falling in the 1kb region centered on the summit. Will plot the number of reads for each fragment length.

Type: Galaxy

Creator: Lucille Delisle

Submitter: Finn Bacall

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