wuyank

EasyFuse

EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.

gatk4-jupyter-notebook-tutorials

This repository contains Jupyter Notebooks containing GATK Best Practices Workflows

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

gatk4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

seq-format-conversion

Workflows for converting between sequence data formats

gatk4-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

RNA-seq

A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample

wdl

Workflow Description Language - Specification and Implementations

Trimmomatic

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

guideseq

Analysis pipeline for the GUIDE-seq assay.

STAR-Fusion

STAR-Fusion codebase

mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

DeepCAT

Deep Learning Method to Identify Cancer Associated TCRs

TRUST4

TCR and BCR assembly from RNA-seq data

seq2HLA

In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.

arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq

HLAProfiler

Using k-mers to call HLA alleles in RNA sequencing data

Biopython-cn

Biopython Tutorial Chinese Translation

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

bget

Portable command-line tool to query bioinformatics APIs, data, databases and files.

Ventoy

A new bootable USB solution.

alphafold

Open source code for AlphaFold.

RoseTTAFold

This package contains deep learning models and related scripts for RoseTTAFold