sanger-tol/ascc sanger-tol/ascc

  • Stars
    star
    3
  • Rank 3,963,521 (Top 79 %)
  • Language Nextflow
  • License
    MIT License
  • Created over 1 year ago
  • Updated 4 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
sanger-tol/ascc
github

sanger-tol

Reviews

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

Repository Details

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

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

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
11

tol-qc

Scripts to generate ToLQC reports for the Sanger Tree of Life programme
Perl
3
star
12

curationpretext

A Nextflow DSL2 pipeline for pretext generation in curation
Nextflow
3
star
13

agp-tpf-utils

Code for manipulating AGP and TPF assembly files
Python
2
star
14

vectorDB

adaptor sequences of Pacbio Hifi reads
2
star
15

tol-track

Tracking scripts for Sanger Tree of Life sequencing data
Perl
2
star
16

PretextSnapshot

Commandline image generator for Pretext contact maps.
C++
2
star
17

docker-images

Perl
2
star
18

asg-assembly-course-2021

Notes for the 2021 Aquatic Symbiosis Genomics assembly course
2
star
19

nf-core-pipeline

Guidelines and subworkflows for Nextflow pipeline development in Sanger ToL
Nextflow
2
star
20

sequencecomposition

Nextflow pipeline to extract statistics from a genome about its sequence composition
Groovy
2
star
21

mergePacBioCCSreports

Merge multiple PacBio CCS report files
Perl
1
star
22

longreadmag

Groovy
1
star
23

ensemblgenedownload

Nextflow pipeline to download gene annotations from Ensembl onto the Tree of Life directory structure
Groovy
1
star
24

ensemblrepeatdownload

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

insdcdownload

Nextflow pipeline to download assemblies from INSDC and add them to the Tree of Life directories
Groovy
1
star