sanger-pathogens / Bio-Tradis
A set of tools to analyse the output from TraDIS analyses
☆23Updated last year
Alternatives and similar repositories for Bio-Tradis:
Users that are interested in Bio-Tradis are comparing it to the libraries listed below
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆52Updated 2 years ago
- visualising sequence similarity with Circos☆39Updated 5 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 3 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆43Updated 4 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆57Updated 11 months ago
- Protein Alignment and Detection Interface☆61Updated 11 months ago
- Automated Sanger Analysis Pipeline (ASAP): a tool for rapidly analyzing Sanger sequencing data with minimum user interference.☆25Updated last month
- ☆31Updated 10 months ago
- A nextflow pipeline for decontamination of short reads, long reads and contigs☆44Updated 2 months ago
- A small bash script that automates sweeping Guppy parameters in an attempt to optimise basecalling rate☆30Updated 2 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated last year
- ☆41Updated 4 years ago
- BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a f…☆34Updated 6 years ago
- IS mapping software☆53Updated 3 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 3 years ago
- An R package designed for drawing gene arrow maps☆63Updated 3 weeks ago
- StrainFinder☆26Updated 6 years ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆53Updated last year
- ☆27Updated 2 months ago
- A toolkit for prokaryotic comparative genomics☆45Updated last month
- HoCoRT - Remove specific organisms from sequencing reads☆17Updated 2 months ago
- Add new taxa or taxonomic groups to the NCBI Taxdump files☆19Updated 5 years ago
- ☆67Updated this week
- A program for detection of tRNA genes☆60Updated 2 years ago
- SHOOT.bio - the phylogenetic search engine☆24Updated last year
- OPAL: Open-community Profiling Assessment tooL☆28Updated last month
- scripts for estimating bacteria replication rates based on population genome copy number variation☆70Updated 5 years ago
- Repository for scripts and resources used for metagenomics with Nanopore, PacBio and Illumina sequencing☆21Updated 2 years ago
- Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…☆31Updated last year