sanger-tol Goto Github PK

.github

GitHub configuration

agp-tpf-utils

Code for manipulating AGP and TPF assembly files

arima_mapping_pipeline

Fork of the mapping pipeline for data generated using Arima-HiC. Sanger Tree of Life modifications

ascc

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

asg-assembly-course-2021

Notes for the 2021 Aquatic Symbiosis Genomics assembly course

bioscan.cog

blobtoolkit

Nextflow pipeline for BlobToolKit for Sanger ToL production suite

curationpretext

A Nextflow DSL2 pipeline for pretext generation in curation

ensemblgenedownload

Nextflow pipeline to download gene annotations from Ensembl onto the Tree of Life directory structure

ensemblrepeatdownload

Nextflow pipeline to download repeat annotations from Ensembl onto the Tree of Life directory structure

gda

Genome Decomposition Analysis pipeline

genealignment

An NF-core pipeline to alignment genesets against a given reference genome.

genomeassembly

Implementation of ToL genome assembly workflows

genomenote

This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

insdcdownload

Nextflow pipeline to download assemblies from INSDC and add them to the Tree of Life directories

longreadmag

mergepacbioccsreports

Merge multiple PacBio CCS report files

minibtk

Nextflow pipeline that runs some of the BTK steps

nf-core-modules

Repository to host Tree of Life's Nextflow DSL2 modules, alongside nf-core's

nf-core-pipeline

Guidelines and subworkflows for Nextflow pipeline development in Sanger ToL

nf-core-tools

Python package with helper tools for the nf-core community.

pipelines-website

Code and files for the sanger-tol pipelines website.

pretextgraph

Embeds bedgraph data into Pretext contact maps.

pretextmap

Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.

pretextsnapshot

Commandline image generator for Pretext contact maps.

pretextview

OpenGL Powered Pretext Contact Map Viewer

readmapping

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

sequencecomposition

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

singularity-hpc

Local filesystem registry for containers (intended for HPC) using Lmod or Environment Modules. Works for users and admins.

software-tracker

API and helper scripts for the pathogen software installation tracking database