wtsi-hpag

Software tools and pipelines developed by the High Performance Algorithms Group @ the Wellcome Sanger Institute

wtsi-hpag's repositories

scanPAV

Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.

Language:CMIT29 3 3

Scaff10X

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Language:CMIT20 5 25

scaffHiC

Pipeline for genome scaffolding by modelling distributions of HiC pairs

Language:CMIT10 2 5

caus

CAUS is a pipeline for Chromosome Assignment Using Synteny

Language:CMIT4 3 2

easyChain

easyChain is a pipeline to produce a chain file from two genome assemblies.

Language:CMIT4 10

HiLine

HiC alignment and classification pipeline

Language:PythonNOASSERTION4 2 2

smis

SMIS: Single Molecular Integrative Scaffolding. A pipeline for scaffolding genome assemblies using long reads (PacBio, ONT)

Language:CGPL-3.04 1 2

SamHaplotag

Process haplotag barcodes in SAM format

Language:C++MIT200

AncesBin

Pipeline to bin 10X, HiC, PacBio and ONT reads based on ancestry assemblies

Language:CMIT1 10

SIMDExtensionWrapper

Generic wrapper program, detects SIMD CPU extensions and launches an appropriate sub-process.

Language:CNOASSERTION1 20

covidPileup

Pipeline for building SNP and GAP pileup from multiple COVID-19 whole genome sequences.

Language:CMIT020

scaffhtag

Pipeline for scaffolding genome assemblies using haplotagging reads

Language:CMIT010

chromoSPA

A Size and Positional Analysis (SPA) tool for studying chromothripsis breakages.

Language:C++MIT010

ContactPointAnalysis

A statistical tool for analysing the Contact Point hypothesis for Chromothripsis

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CoverageWorkshop

A Workshop Notebook used for running a session as part of the OpenLab series.

Language:Jupyter Notebook000

GenCHORD

A Bayesian method to smooth-out the noise in a coverage dataset, revealing the underlying average behaviour which is constrained to lie on `Harmonics' of a fundamental coverage value.

Language:C++GPL-3.0000

HypoCoverage

Coverage Analysis Tools

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HypothesisTester

A Bayesian Statistical Inference framework for comparing hypotheses

Language:C++010

LinkStats

Collect and process statistics from aligned linked-reads.

Language:CNOASSERTION010

MCSampler

An MCMC Sampling framework for sampling from arbitrary probability densities.

Language:C++000

stepStone

A pipeline for identification of chromothripsis breakpoints and cancer rearrangements

Language:CMIT000

varibase

A pipeline to correct variation errors of SNPs/indles from genome assembly

Language:CMIT010