28 sanger-tol/treeval

curation genome-alignment genome-assembly genomics quality-control synteny

Pipelines for the production of Treeval data

Version 1.4.2   Published 3 days ago

13 sanger-tol/curationpretext

genomics hic

A Nextflow DSL2 pipeline for pretext generation in curation

Version 1.5.1   Published 4 days ago

5 sanger-tol/ascc

genomics

A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.

Version 0.5.2   Published 7 days ago

13 sanger-tol/blobtoolkit

blobtools decontamination genomehubs genomics

Nextflow DSL2 pipeline to generate data for a BlobToolKit analysis. This workflow is part of the Tree of Life production suite.

Version 0.9.0   Published 1 week ago

sanger-tol/nfmicrofinder

This pipeline aids the curation of bird genome assemblies by identifying putative microchromosome scaffolds and moving them to the start of the genome assembly FASTA file.

Version 1.0.0   Published 2 weeks ago

3 sanger-tol/metagenomeassembly

A Nextflow pipeline for the assembly and binning of metagenomes from PacBio HiFi and Illumina Hi-C sequencing data.

Version 1.2.0   Published 3 weeks ago

9 sanger-tol/variantcalling

alignment genomics variant-calling

Nextflow DSL2 pipeline to call variants on long read alignment.

Version 1.1.9-himut.2   Published 3 weeks ago

26 sanger-tol/genomenote

genomics hic publications statistics

Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.

Version 1.2.6   Published 3 months ago

13 sanger-tol/readmapping

genomics read-alignment

Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.

Version 1.3.4   Published 7 months ago

sanger-tol/ear

genomics reporting-tool

ERGA Assembly Report pipeline

Version 0.6.2   Published 9 months ago

2 sanger-tol/sequencecomposition

genomics kmer-frequency-count running-average shannon-entropy

Nextflow DSL2 pipeline to extract statistics from a genome about its sequence composition

Version 1.1.0   Published 10 months ago

1 sanger-tol/ensemblrepeatdownload

download formatting genomics

Nextflow DSL2 pipeline to download repeat annotations from Ensembl.

Version 2.0.1   Published 10 months ago

1 sanger-tol/ensemblgenedownload

download gene-annotation genomics indexing

Nextflow DSL2 pipeline to download gene annotations from Ensembl.

Version 2.0.2   Published 10 months ago

1 sanger-tol/insdcdownload

download genomics indexing

Nextflow DSL2 pipeline to download assemblies from INSDC.

Version 2.0.2   Published 10 months ago