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Search results for next generation sequencing
next-generation-sequencing
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74 search results found
Jvarkit
⭐
440
Java utilities for Bioinformatics
Awosome Bioinformatics
⭐
366
A curated list of resources for learning bioinformatics.
Sarek
⭐
299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Kaiju
⭐
236
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Ngmlr
⭐
230
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
Roary
⭐
219
Rapid large-scale prokaryote pan genome analysis
Circlator
⭐
193
A tool to circularize genome assemblies
Artemis
⭐
191
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Nextclade
⭐
190
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
Snp Sites
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173
Finds SNP sites from a multi-FASTA alignment file
Ngless
⭐
141
NGLess: NGS with less work
Ariba
⭐
135
Antimicrobial Resistance Identification By Assembly
Gubbins
⭐
133
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Sarek
⭐
126
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
Fqtools
⭐
105
An efficient FASTQ manipulation suite
Rvtests
⭐
95
Rare variant test software for next generation sequencing data
Snpgenie
⭐
94
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
Assembly Stats
⭐
92
Get assembly statistics from FASTA and FASTQ files
Ngseasy
⭐
76
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
Czid Web
⭐
75
Infectious Disease Sequencing Platform
Atacseq
⭐
64
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
Msisensor Pro
⭐
63
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
Deepmicrobes
⭐
61
DeepMicrobes: taxonomic classification for metagenomics with deep learning
Fq
⭐
54
Command line utility for manipulating Illumina-generated FASTQ files.
Htstream
⭐
48
A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes
Fastaq
⭐
45
Python3 scripts to manipulate FASTA and FASTQ files
Assembly_improvement
⭐
39
Improve the quality of a denovo assembly by scaffolding and gap filling
Pathogen Informatics Training
⭐
38
Iva
⭐
37
de novo virus assembler of Illumina paired reads
Oliver
⭐
36
An opinionated Cromwell orchestration manager.
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.
Advntr
⭐
35
A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
Cloops2
⭐
32
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
Workflows
⭐
28
Bioinformatics workflows developed for and used on the St. Jude Cloud project.
Seqminer
⭐
28
Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R
Wdldoc
⭐
26
Create WDL documentation using Markdown.
Omicselector
⭐
26
OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.
Ngstools
⭐
23
My own tools code for NGS data analysis (Next Generation Sequencing)
Cacao
⭐
22
Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
Pm4ngs
⭐
21
Project Manager for NGS data analysis
Samstat
⭐
20
SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.
Gff3toembl
⭐
20
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Yleaf
⭐
19
Yleaf software for human Y-chromosomal haplogroup inference from next generation sequencing data
Mspc
⭐
18
Using combined evidence from replicates to evaluate ChIP-seq peaks
Phat
⭐
17
Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
Icallsv
⭐
16
A Framework to call Structural Variants from NGS based datasets
Plasmidtron
⭐
16
Assembling the cause of phenotypes and genotypes from NGS data
Bio Tradis
⭐
15
A set of tools to analyse the output from TraDIS analyses
Informme
⭐
15
An information-theoretic pipeline for methylation analysis of WGBS data
Minorseq
⭐
14
Minor Variant Calling and Phasing Tools
Mlst_check
⭐
14
Multilocus sequence typing by blast using the schemes from PubMLST
Saffrontree
⭐
14
SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
Sandy
⭐
14
A straightforward and complete next-generation sequencing read simulator
Seroba
⭐
14
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
Angsd Wrapper
⭐
13
Utilities for analyzing next generation sequencing data.
Sequence_handling
⭐
12
A series of scripts to automate sequence workflows
Lodestone
⭐
11
Mycobacterial pipeline
Sigalign
⭐
10
A Similarity-Guided Alignment Algorithm
Ngsderive
⭐
10
Forensic analysis tool useful in backwards computing information from next-generation sequencing data.
Ngsphy
⭐
9
NGSphy: phylogenomic simulation of next-generation sequencing data
Py4lifesci
⭐
9
Code repository for the book "Python for the Life Sciences" by Lancaster & Webster
Captus
⭐
8
Assembly of Phylogenomic Datasets from High-Throughput Sequencing data
Plethora
⭐
8
Copy number estimation of highly duplicated sequences
Massgenotyping
⭐
7
Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data
Albatradis
⭐
7
Comparative TraDIS analysis
Docs
⭐
7
Documentation on St. Jude Cloud.
Sentieon Dnascope Ml
⭐
7
Sentieon DNAscope + Machine Learning Model
Rust Msbwt
⭐
7
place for building up a msbwt resource in Rust
Sideretro
⭐
7
A pipeline for detecting Somatic Insertion of DE novo RETROcopies
Dhtslib
⭐
6
D bindings and OOP wrappers for htslib
Metadatatable
⭐
5
Work on and around an interactive metadata table for project identification
Deepmicrobes
⭐
5
DeepMicrobes: a deep learning architecture for taxonomic classification of shotgun metagenomic reads
Cnvetti
⭐
5
🎉 CNVetti – robust, efficient, and versatile clinical CNV calling from HTS data
Genocraft
⭐
5
GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization
1-74 of 74 search results
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