sanger-tol/insdcdownload sanger-tol/insdcdownload

  • Stars
    star
    1
  • Language
    Groovy
  • License
    MIT License
  • Created over 2 years ago
  • Updated 5 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
sanger-tol/insdcdownload
github

sanger-tol

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

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

More Repositories

1

PretextView

OpenGL Powered Pretext Contact Map Viewer
C
27
star
2

genomenote

This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.
Groovy
21
star
3

treeval

Pipelines for the production of Treeval data
Nextflow
20
star
4

PretextMap

Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.
C
18
star
5

genomeassembly

Implementation of ToL genome assembly workflows
Nextflow
13
star
6

blobtoolkit

Nextflow pipeline for BlobToolKit for Sanger ToL production suite
Nextflow
11
star
7

readmapping

Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.
Nextflow
8
star
8

gda

Genome Decomposition Analysis pipeline
Python
4
star
9

tolqc

ToLQC API and website. This is a mirror of the GitLab repository - please don't commit to this repo.
Python
3
star
10

ascc

A Nextflow DSL2 pipeline for the identification of cobiont and contaminating sequences using fasta and pacbio data.
Nextflow
3
star
11

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.
Nextflow
3
star
12

tol-qc

Scripts to generate ToLQC reports for the Sanger Tree of Life programme
Perl
3
star
13

curationpretext

A Nextflow DSL2 pipeline for pretext generation in curation
Nextflow
3
star
14

agp-tpf-utils

Code for manipulating AGP and TPF assembly files
Python
2
star
15

vectorDB

adaptor sequences of Pacbio Hifi reads
2
star
16

tol-track

Tracking scripts for Sanger Tree of Life sequencing data
Perl
2
star
17

PretextSnapshot

Commandline image generator for Pretext contact maps.
C++
2
star
18

docker-images

Perl
2
star
19

asg-assembly-course-2021

Notes for the 2021 Aquatic Symbiosis Genomics assembly course
2
star
20

nf-core-pipeline

Guidelines and subworkflows for Nextflow pipeline development in Sanger ToL
Nextflow
2
star
21

sequencecomposition

Nextflow pipeline to extract statistics from a genome about its sequence composition
Groovy
2
star
22

mergePacBioCCSreports

Merge multiple PacBio CCS report files
Perl
1
star
23

longreadmag

Groovy
1
star
24

ensemblgenedownload

Nextflow pipeline to download gene annotations from Ensembl onto the Tree of Life directory structure
Groovy
1
star
25

ensemblrepeatdownload

Nextflow pipeline to download repeat annotations from Ensembl onto the Tree of Life directory structure
Groovy
1
star