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48 search results found

Jvarkit ⭐ 440

Java utilities for Bioinformatics

Awosome Bioinformatics ⭐ 366

A curated list of resources for learning bioinformatics.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

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

Snp Sites ⭐ 173

Finds SNP sites from a multi-FASTA alignment file

NGLess: NGS with less work

Antimicrobial Resistance Identification By Assembly

Gubbins ⭐ 133

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Fqtools ⭐ 105

An efficient FASTQ manipulation suite

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

Czid Web ⭐ 75

Infectious Disease Sequencing Platform

Deepmicrobes ⭐ 61

DeepMicrobes: taxonomic classification for metagenomics with deep learning

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

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

de novo virus assembler of Illumina paired reads

An opinionated Cromwell orchestration manager.

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data

Workflows ⭐ 28

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

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.

Create WDL documentation using Markdown.

Ngstools ⭐ 23

My own tools code for NGS data analysis (Next Generation Sequencing)

Project Manager for NGS data analysis

Gff3toembl ⭐ 20

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Plasmidtron ⭐ 16

Assembling the cause of phenotypes and genotypes from NGS data

A Framework to call Structural Variants from NGS based datasets

Informme ⭐ 15

An information-theoretic pipeline for methylation analysis of WGBS data

Bio Tradis ⭐ 15

A set of tools to analyse the output from TraDIS analyses

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

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

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.

Py4lifesci ⭐ 9

Code repository for the book "Python for the Life Sciences" by Lancaster & Webster

Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Documentation on St. Jude Cloud.

Albatradis ⭐ 7

Comparative TraDIS analysis

D bindings and OOP wrappers for htslib

🎉 CNVetti – robust, efficient, and versatile clinical CNV calling from HTS data

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