Peng Jia's repositories
NGSGermlineMutPipe
Germline mutation pipeline
TGSGermlineMutPipe
Germline mutations detection pipeline with long reads
pengjia.github.io
Github pages
pindel_complex
capture complex events based on pindel
bioconda-recipes
Conda recipes for the bioconda channel.
cluster
Instructions of HPC at Ye-lab
edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
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HPP_Year1_Assemblies
Assemblies from HPP Year 1 production
igv-reports
Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol.
msisensor-pro
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
msisensor-rna
MSIRNA: Microsatellite instability detection using RNA sequencing data
pindel
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
playground
Small tools to improve efficiency.
pyCircos
python Circos
STRling
Detect novel (and reference) STR expansions from short-read data
truvari
Structural variant toolkit for VCFs