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50 search results found

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

Gcp For Bioinformatics ⭐ 178

GCP for Bioinformatics Researchers

Snp Sites ⭐ 173

Finds SNP sites from a multi-FASTA alignment file

Gubbins ⭐ 154

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

NGLess: NGS with less work

Antimicrobial Resistance Identification By Assembly

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Open Cravat ⭐ 98

A modular annotation tool for genomic variants

Czid Web ⭐ 75

Infectious Disease Sequencing Platform

Awesome Structural Bioinformatics ⭐ 54

Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.

Phigaro is a scalable command-line tool for predicting phages and prophages

Bystro genetic analysis (annotation, filtering, statistics)

Assembly_improvement ⭐ 39

Improve the quality of a denovo assembly by scaffolding and gap filling

de novo virus assembler of Illumina paired reads

An opinionated Cromwell orchestration manager.

Order and orientation of complete bacterial genomes

Gff3toembl ⭐ 20

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

Predict plasmids from uncorrected long read data

Kgwasflow ⭐ 19

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Make_lastz_chains ⭐ 17

Portable solution to generate genome alignment chains using lastz

Hicstuff ⭐ 17

Simple library/pipeline to generate and handle Hi-C data.

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

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

Saffrontree ⭐ 14

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Mlst_check ⭐ 14

Multilocus sequence typing by blast using the schemes from PubMLST

Edgecase ⭐ 13

A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

Region Plot ⭐ 12

A tool to plot significant regions of GWAS

Lodestone ⭐ 11

Mycobacterial pipeline

Bioinformatics Toolbox ⭐ 10

Docker container for bioinformatics tools and pipelines

Positive Selection ⭐ 10

Scripts and procedures for detecting positively selected genes and codons in primates

Bioinformatics ⭐ 10

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.

This project proposes to contribute to fill the knowledge gap about Covid-19SARS-CoV-2 in Brazil and with the global knowledge about the pathogen. The scientific community and governments of other countries are looking for actions along these lines. The United Kingdom recently established a research network for genomic studies of SARS-CoV-2Covid-19 with a contribution of GBP 20 million (https://www.gov.uk/government/news/uk-launches-wh genome-sequence-alliance-to-map-spread-of-coronavi

Python Library for data analysis based on GMQL

Riboraptor ⭐ 9

Tool for ribo-seq analysis

PCA on Genotypes

A suite of unique bioinformatics tools for the brave explorer.

Albatradis ⭐ 7

Comparative TraDIS analysis

Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.

Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

Toolkit for analysis of ".hyb" format nucleotide sequence data from chimeric RNA experiments.

Kas Analyzer ⭐ 6

New computational framework to process and analyze KAS-seq and spKAS-seq data.

Recenthgt ⭐ 5

A novel bioinformatics pipeline for recent horizontal gene transfer detecting.

AllMine, a flexible pipeline for Allele Mining. Develloped at INRA's GAFL unit :

Fungal Wdl ⭐ 5

Broad fungal method repository

Recimap (a reciprocal mapping tool) was developed as a bioinformatics command-line tool/pipeline to find rearrangements breakpoints between two closely related genomes.

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Python Bioinformatics Pipeline (114)

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