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400 search results found
Deepvariant
⭐
2,978
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Fastp
⭐
1,602
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging.
Gatk
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1,576
Official code repository for GATK versions 4 and up
Ngs
⭐
1,252
Next Generation Shell (NGS)
Galaxy
⭐
1,211
Data intensive science for everyone.
Sra Tools
⭐
1,015
SRA Tools
Htslib
⭐
762
C library for high-throughput sequencing data formats
Deeptools
⭐
644
Tools to process and analyze deep sequencing data.
Awesome Omics
⭐
536
A collection of awesome things regarding all omics.
Jvarkit
⭐
440
Java utilities for Bioinformatics
Snakepipes
⭐
359
Customizable workflows based on snakemake and python for the analysis of NGS data
Bioconvert
⭐
344
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
Juicer
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313
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Fgbio
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292
Tools for working with genomic and high throughput sequencing data.
Training Material
⭐
284
A collection of Galaxy-related training material
Htsjdk
⭐
271
A Java API for high-throughput sequencing data (HTS) formats.
Ngsplot
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231
Quick mining and visualization of NGS data by integrating genomic databases
Python Musicbrainzngs
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222
Python bindings for Musicbrainz' NGS webservice
Sortmerna
⭐
220
SortMeRNA: next-generation sequence filtering and alignment tool
Cooler
⭐
191
A cool place to store your Hi-C
Ugene
⭐
190
UGENE is free open-source cross-platform bioinformatics software
Annotsv
⭐
180
Annotation and Ranking of Structural Variation
Scde
⭐
163
R package for analyzing single-cell RNA-seq data
Afterqc
⭐
157
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Ngb
⭐
151
New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support
Ngstools
⭐
142
Programs to analyse NGS data for population genetics purposes
Ngless
⭐
141
NGLess: NGS with less work
Cloud Pipeline
⭐
137
Cloud agnostic genomics analysis, scientific computation and storage platform
Sequana
⭐
136
Sequana: a set of Snakemake NGS pipelines
Seq2science
⭐
132
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
Viral Ngs
⭐
129
Viral genomics analysis pipelines
Mutscan
⭐
127
Detect and visualize target mutations by scanning FastQ files directly
Ngs Bits
⭐
121
Short-read sequencing tools
V Pipe
⭐
119
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Atropos
⭐
116
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
Ngs
⭐
114
NGS Language Bindings
Crispresso
⭐
110
Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data
Ngscheckmate
⭐
106
Software program for checking sample matching for NGS data
Gencore
⭐
103
Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
Cloops
⭐
99
Accurate and flexible loops calling tool for 3D genomic data.
Ngs Tools
⭐
99
Isoquant
⭐
98
Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
Reg Gen
⭐
96
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Seqfu2
⭐
96
🚀 seqfu - Sequece Fastx Utilities
Rvtests
⭐
95
Rare variant test software for next generation sequencing data
Platon
⭐
93
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
Bwa Meme
⭐
92
BWA-MEME: Faster BWA-MEM2 using learned-index
Tadbit
⭐
89
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
Ngs Pipe
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87
NGS-pipe: next-generation sequencing pipelines for precision oncology
Bamnostic
⭐
84
a pure Python multi-version tolerant, runtime and OS-agnostic Binary Alignment Map (BAM) file parser and random access tool
Mcclintock
⭐
83
Meta-pipeline to identify transposable element insertions using next generation sequencing data
Recentrifuge
⭐
83
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
Player2d
⭐
83
Educational demo implementing a swept 2D character controller
Tbprofiler
⭐
81
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
Spark
⭐
81
Publication quality NGS track plotting
Genomics
⭐
78
Scripts, utilities and programs for genomic bioinformatics.
Callings Nf
⭐
76
GATK RNA-Seq Variant Calling in Nextflow
Ngseasy
⭐
76
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
Tpmcalculator
⭐
74
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
Trimmomatic
⭐
74
Read trimming tool for Illumina NGS data.
Abra2
⭐
69
ABRA2
Clincnv
⭐
65
Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
Haplogrep Cmd
⭐
64
HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
Catch
⭐
63
A package for designing compact and comprehensive capture probe sets.
Iskylims
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61
is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.
Opengene.jl
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61
(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Precisionfda
⭐
57
precisionFDA is a cloud based platform that provides an environment where the community can test, pilot, and benchmark new approaches to validating their next-generation sequencing (NGS) analysis pipelines. PrecisionFDA offers community members a secure and independent work area where, at their discretion, their bioinformatics tools or data can be kept private or shared with the precisionFDA participants.
Fastv
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56
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.
Burst
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54
An ultrafast optimal aligner for mapping large NGS data to large genome databases.
Bayestyper
⭐
52
A method for variant graph genotyping based on exact alignment of k-mers
Rapt
⭐
51
Read Assembly and Annotation Pipeline Tool
Fastq And Furious
⭐
49
Efficient handling of FASTQ files from Python
Main
⭐
49
Viral Pipelines
⭐
48
viral-ngs: complete pipelines
Impact Pipeline
⭐
47
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
Hlaminer
⭐
46
⛏HLA predictions from NGS shotgun data
Asap
⭐
46
A scalable bacterial genome assembly, annotation and analysis pipeline
Community_software_tools_for_ngs
⭐
46
Systempiper
⭐
45
Project Website:
Seqmonk
⭐
45
SeqMonk NGS visualisation and analysis tool
Pipeliner
⭐
44
An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.
Grabseqs
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44
A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
Snpsplit
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43
Allele-specific alignment sorting
Bamtocov
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43
🏔 coverage extraction from BAM/CRAM files, supporting targets 📊
Struo2
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42
Scalable creating/updating of metagenome profiling databases
Fastq Screen
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42
Detecting contamination in NGS data and multi-species analysis
Cfdnapattern
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42
Pattern Recognition for Cell-free DNA
Ngs Primerplex
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42
NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design
Struo
⭐
40
Ley Lab MetaGenome Profiler DataBase generator
Consent
⭐
40
Scalable long read self-correction and assembly polishing with multiple sequence alignment
Migec
⭐
40
A RepSeq processing swiss-knife
Needlestack
⭐
39
Multi-sample somatic variant caller
Circle Map
⭐
39
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
Gamgee
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39
A C++14 library for NGS data formats
Ococo
⭐
39
Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
Migmap
⭐
38
HTS-compatible wrapper for IgBlast V-(D)-J mapping tool
Pcangsd
⭐
38
Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
Ngstools
⭐
37
Next-Generation Sequencing(NGS) toolkits.
Mapdamage
⭐
37
mapDamage: tracking and quantifying damage patterns in ancient DNA sequences
Dnascan
⭐
36
DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.
Related Searches
Python Ngs (261)
Sequencing Ngs (182)
Bioinformatics Ngs (165)
Pipeline Ngs (143)
Genome Ngs (115)
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