OpenGene - Open Source Genomics Toolbox

fastp

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

awesome-bio-datasets

awesome-bio-datasets

AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

MutScan

Detect and visualize target mutations by scanning FastQ files directly

repaq

A fast lossless FASTQ compressor with ultra-high compression ratio

GeneFuse

Gene fusion detection and visualization

gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

scrnapip

A Systematic and Dynamic Pipeline for Single-Cell RNA Sequencing Analysis

OpenGene.jl

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

CfdnaPattern

Pattern Recognition for Cell-free DNA

UniqueKMER

Generate unique KMERs for every contig in a FASTA file

ctdna-pipeline

A simplified pipeline for ctDNA sequencing data analysis

VisualMSI

Detect and visualize microsatellite instability(MSI) from NGS data

defq

Please switch to https://github.com/OpenGene/defastq

MrBam

Query Mutated Reads from a Bam

FusionDirect.jl

(No maintenance) Detect gene fusion directly from raw fastq files

SeqMaker.jl

(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated

dedup

Deduplication for cfDNA sequencing data

pecheck

check paired-end FASTQ data integrity

slicer

Slice a text file (like FastQ) to smaller files by lines, with gzip supported

defastq

Ultra-fast Multi-threaded FASTQ Demultiplexing

ACMSI

The shiny-based app for Fragment Analysis, especially for MSI analysis

novelbio-base

novelbio-bioinfo

IRDProc

Process genomic data downloaded from influenza research database for unique k-mer generating