• Stars
    star
    5
  • Rank 2,861,937 (Top 57 %)
  • Language
    Python
  • License
    GNU Affero Genera...
  • Created almost 4 years ago
  • Updated 7 months ago

Reviews

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

Repository Details

Variant Library Annotation Tool (VaLiAnT) is an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments

More Repositories

1

ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing
Perl
67
star
2

CaVEMan

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib
C
60
star
3

BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
Perl
57
star
4

cgpBattenberg

Battenberg algorithm and associated implementation script
Perl
51
star
5

alleleCount

Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)
C
43
star
6

dockstore-cgpwgs

Dockstore implementation of CGP core WGS analysis
Shell
30
star
7

cgpBigWig

BigWig manpulation tools using libBigWig and htslib
C
28
star
8

cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
Perl
27
star
9

ClusterSV

SV clustering
R
25
star
10

vafCorrect

Calculates the Variant Allele Fraction of variants in VCF files
Perl
19
star
11

telomerecat

Telomerecat: The telomere computational analysis tool
Python
17
star
12

NanoSeq

Analysis software for Nanorate Sequencing (NanoSeq) experiments
C++
12
star
13

SimSvGenomes

Simulation of somatically rearranged genomes
C
9
star
14

PCAP-core

NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)
Perl
9
star
15

VAGrENT

A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences
Perl
8
star
16

dockstore-cgpmap

Mapping using PCAP
Common Workflow Language
6
star
17

cgpCaVEManWrapper

Reference implementation of CGP workflow for CaVEMan SNV analysis
Perl
6
star
18

cgpRna

Perl
5
star
19

grass

Gene Rearrangement AnalySiS
Perl
4
star
20

pyCRISPRcleanR

Python version of CRISPRcleanR: An R package for unsupervised identification and correction of gene independent cell responses to CRISPR-cas9 targeting
Python
4
star
21

AutoCSA

LEGACY: AutoCSA (Automatic Comparative Sequence Analysis) is a mutation detection program designed to detect small mutations (1-50 bases) in capillary sequence traces. The software is capable of detecting both homozygous and heterozygous base substitutions, as well as small insertions and deletions, to a high sensitivity.
Java
4
star
22

dockstore-cgpwxs

Dockstore implementation of CGP core WXS analysis
Shell
3
star
23

cgpNgsQc

Collection of code for checking NSG sequencing results
Perl
3
star
24

cgpbox

DEPRECATED please see dockstore-cgpwgs
JavaScript
3
star
25

proportionalmultibw

JBrowse plugin to display multiple BigWig tracks as a stacked proportion
JavaScript
3
star
26

strelka2-manta

Container for strelka2 and manta
Dockerfile
2
star
27

RCRISPR

R library for CRISPR analysis
R
2
star
28

cgpCaVEManPostProcessing

Flagging add on to CaVEMan
Perl
2
star
29

ppcg-qc-from-sanger

The tools is used to extract PPCG defined QC metrics from Sanger variant calling pipeline results.
Python
2
star
30

telomerehunter-docker

Repository to generate docker image for telomerehunter
Dockerfile
2
star
31

PerlSvAnalysisLib

Object-oriented Perl library for somatic rearrangement analysis
Perl
2
star
32

WwDocker

(WildWest) Docker - Docker host manager using RabbitMQ
Java
2
star
33

vcf_flag_modifier

Python application to remove specific flags from VCF files
Python
1
star
34

gripss

Container for the GRIPSS filtering tool ( hartwigmedical / hmftools) for filtering GRIDSS resutls
Dockerfile
1
star
35

pycroquet

python Crispr Read to Oligo QUantification and Evaluation Tool
Jupyter Notebook
1
star
36

cgpAnalyseHub

Tools to automate CGHub repository download and process with CGP analysis pipelines.
Perl
1
star
37

C-SAR

Data will be added ahead of poster/conference
Nextflow
1
star
38

sPlot

Supporting code for Sequence and somatic variation plots
Perl
1
star
39

docker-sigprofiler

Python
1
star
40

cgpJBrowseToolkit

Holds publicly useful scripts and tools for JBrowse users and admins
JavaScript
1
star
41

dockstore-biobambam2

Dockstore implementation of bamtofastq (biobambam2)
Shell
1
star
42

CASM-Smart-Phase

Docker and associated CASM utility scripts for Smart-Phase (https://github.com/paulhager/smart-phase)
Python
1
star
43

TraFiC

DEPRECATED please see https://gitlab.com/mobilegenomes/TraFiC
Perl
1
star
44

pygas

python Guide aligned Sequences
Python
1
star
45

BRASS-wdl

WDL descriptor for BRASS
WDL
1
star
46

QUANTS

Python
1
star
47

cgp-dockstore

Contains scripts and packer builds for cgp-dockstore and Openstack builds
Shell
1
star
48

kourami-docker

Dockerfile for Kourami assembler for HLA haplotypes
Shell
1
star
49

crisprReadCountsPy

A tool to count reads for CRISPR.
Python
1
star