wtsi-hpag
Software tools and pipelines developed by the High Performance Algorithms Group @ the Wellcome Sanger Institute
Pinned Repositories
AncesBin
Pipeline to bin 10X, HiC, PacBio and ONT reads based on ancestry assemblies
caus
CAUS is a pipeline for Chromosome Assignment Using Synteny
easyChain
easyChain is a pipeline to produce a chain file from two genome assemblies.
HiLine
HiC alignment and classification pipeline
SamHaplotag
Process haplotag barcodes in SAM format
Scaff10X
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
scaffHiC
Pipeline for genome scaffolding by modelling distributions of HiC pairs
scanPAV
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
SIMDExtensionWrapper
Generic wrapper program, detects SIMD CPU extensions and launches an appropriate sub-process.
smis
SMIS: Single Molecular Integrative Scaffolding. A pipeline for scaffolding genome assemblies using long reads (PacBio, ONT)
wtsi-hpag's Repositories
wtsi-hpag/scanPAV
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
wtsi-hpag/Scaff10X
Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads
wtsi-hpag/scaffHiC
Pipeline for genome scaffolding by modelling distributions of HiC pairs
wtsi-hpag/caus
CAUS is a pipeline for Chromosome Assignment Using Synteny
wtsi-hpag/easyChain
easyChain is a pipeline to produce a chain file from two genome assemblies.
wtsi-hpag/HiLine
HiC alignment and classification pipeline
wtsi-hpag/smis
SMIS: Single Molecular Integrative Scaffolding. A pipeline for scaffolding genome assemblies using long reads (PacBio, ONT)
wtsi-hpag/SamHaplotag
Process haplotag barcodes in SAM format
wtsi-hpag/AncesBin
Pipeline to bin 10X, HiC, PacBio and ONT reads based on ancestry assemblies
wtsi-hpag/SIMDExtensionWrapper
Generic wrapper program, detects SIMD CPU extensions and launches an appropriate sub-process.
wtsi-hpag/covidPileup
Pipeline for building SNP and GAP pileup from multiple COVID-19 whole genome sequences.
wtsi-hpag/scaffhtag
Pipeline for scaffolding genome assemblies using haplotagging reads
wtsi-hpag/chromoSPA
A Size and Positional Analysis (SPA) tool for studying chromothripsis breakages.
wtsi-hpag/ContactPointAnalysis
A statistical tool for analysing the Contact Point hypothesis for Chromothripsis
wtsi-hpag/CoverageWorkshop
A Workshop Notebook used for running a session as part of the OpenLab series.
wtsi-hpag/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.
wtsi-hpag/HypoCoverage
Coverage Analysis Tools
wtsi-hpag/HypothesisTester
A Bayesian Statistical Inference framework for comparing hypotheses
wtsi-hpag/LinkStats
Collect and process statistics from aligned linked-reads.
wtsi-hpag/MCSampler
An MCMC Sampling framework for sampling from arbitrary probability densities.
wtsi-hpag/stepStone
A pipeline for identification of chromothripsis breakpoints and cancer rearrangements
wtsi-hpag/varibase
A pipeline to correct variation errors of SNPs/indles from genome assembly