OpenGene - Open Source Genomics Toolbox (@OpenGene)
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OpenGene

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  • Stars
    star
    3,330
  • Global Org. Rank 6,425 (Top 3 %)
  • Registered almost 9 years ago
  • Most used languages
    C
         28.0 %
    Python
         20.0 %
    C++
         20.0 %
    Julia
         12.0 %
    Java
         8.0 %
    Shell
         4.0 %
    HTML
         4.0 %
    R
         4.0 %

Top repositories

1

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
C++
1,840
star
2

awesome-bio-datasets

awesome-bio-datasets
211
star
3

AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Python
203
star
4

MutScan

Detect and visualize target mutations by scanning FastQ files directly
C
148
star
5

repaq

A fast lossless FASTQ compressor with ultra-high compression ratio
C
122
star
6

GeneFuse

Gene fusion detection and visualization
C
114
star
7

gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
C++
111
star
8

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.
C++
110
star
9

scrnapip

A Systematic and Dynamic Pipeline for Single-Cell RNA Sequencing Analysis
HTML
98
star
10

OpenGene.jl

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Julia
64
star
11

CfdnaPattern

Pattern Recognition for Cell-free DNA
Python
58
star
12

UniqueKMER

Generate unique KMERs for every contig in a FASTA file
C
43
star
13

ctdna-pipeline

A simplified pipeline for ctDNA sequencing data analysis
Shell
36
star
14

VisualMSI

Detect and visualize microsatellite instability(MSI) from NGS data
C++
31
star
15

defq

Please switch to https://github.com/OpenGene/defastq
C
28
star
16

MrBam

Query Mutated Reads from a Bam
Python
26
star
17

FusionDirect.jl

(No maintenance) Detect gene fusion directly from raw fastq files
Julia
25
star
18

SeqMaker.jl

(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
Julia
24
star
19

dedup

Deduplication for cfDNA sequencing data
Python
10
star
20

defastq

Ultra-fast Multi-threaded FASTQ Demultiplexing
C++
7
star
21

pecheck

check paired-end FASTQ data integrity
C
6
star
22

slicer

Slice a text file (like FastQ) to smaller files by lines, with gzip supported
C
6
star
23

ACMSI

The shiny-based app for Fragment Analysis, especially for MSI analysis
R
4
star
24

novelbio-bioinfo

Java
2
star
25

novelbio-base

Java
2
star
26

IRDProc

Process genomic data downloaded from influenza research database for unique k-mer generating
Python
1
star