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afterqc

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

awesome-bio-datasets

awesome-bio-datasets

cfdnapattern

Pattern Recognition for Cell-free DNA

ctdna-pipeline

A simplified pipeline for ctDNA sequencing data analysis

dedup

Deduplication for cfDNA sequencing data

defastq

Ultra-fast Multi-threaded FASTQ Demultiplexing

defq

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

fastp

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

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.

fusiondirect.jl

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

gencore

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

genefuse

Gene fusion detection and visualization

irdproc

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

mrbam

Query Mutated Reads from a Bam

mutscan

Detect and visualize target mutations by scanning FastQ files directly

novelbio-base

novelbio-bioinfo

opengene.jl

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

pecheck

check paired-end FASTQ data integrity

repaq

A fast lossless FASTQ compressor with ultra-high compression ratio

scrnapip

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

seqmaker.jl

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

slicer

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

uniquekmer

Generate unique KMERs for every contig in a FASTA file

visualmsi

Detect and visualize microsatellite instability(MSI) from NGS data