sanger-tol/PretextMap

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Created over 5 years ago
Updated over 2 years ago

sanger-tol/PretextMap

sanger-tol

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

PretextView

OpenGL Powered Pretext Contact Map Viewer

genomenote

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

treeval

Pipelines for the production of Treeval data

genomeassembly

Implementation of ToL genome assembly workflows

blobtoolkit

Nextflow pipeline for BlobToolKit for Sanger ToL production suite

readmapping

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

gda

Genome Decomposition Analysis pipeline

tolqc

ToLQC API and website. This is a mirror of the GitLab repository - please don't commit to this repo.

ascc

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

variantcalling

This Nextflow DSL2 pipeline calls variants on long read alignment. It is run after sanger-tol/readmapping in the Sanger ToL production suite but with options to run on unaligned reads.

tol-qc

Scripts to generate ToLQC reports for the Sanger Tree of Life programme

curationpretext

A Nextflow DSL2 pipeline for pretext generation in curation

agp-tpf-utils

Code for manipulating AGP and TPF assembly files

vectorDB

adaptor sequences of Pacbio Hifi reads

tol-track

Tracking scripts for Sanger Tree of Life sequencing data

PretextSnapshot

Commandline image generator for Pretext contact maps.

docker-images

asg-assembly-course-2021

Notes for the 2021 Aquatic Symbiosis Genomics assembly course

nf-core-pipeline

Guidelines and subworkflows for Nextflow pipeline development in Sanger ToL

sequencecomposition

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

mergePacBioCCSreports

Merge multiple PacBio CCS report files

longreadmag

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

insdcdownload

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