chiulab / surpi
SURPI
☆84Updated 8 years ago
Alternatives and similar repositories for surpi:
Users that are interested in surpi are comparing it to the libraries listed below
- Updated Kraken DB install scripts to cope with new-ish NCBI structure☆46Updated 7 years ago
- ☆82Updated last year
- ONT assembly and Illumina polishing pipeline☆91Updated 4 years ago
- MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumin…☆44Updated 9 months ago
- qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.☆80Updated 4 years ago
- ☆78Updated 4 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆70Updated 3 years ago
- LoFreq Star: Sensitive variant calling from sequencing data☆105Updated 2 years ago
- Long-read mock community experiments☆105Updated 3 years ago
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated last year
- DDBJ Fast Annotation and Submission Tool☆80Updated last week
- IS mapping software☆54Updated 3 years ago
- This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye…☆58Updated 4 years ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆54Updated 3 years ago
- Fast k-mer based tool for multi locus sequence typing (MLST)☆44Updated 4 years ago
- Edinburgh Genomics MinION training 2016☆33Updated 8 years ago
- a collection of scripts for organising bacterial genomes by species☆76Updated 3 years ago
- Development version of Easyfig☆94Updated last year
- nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…☆69Updated 2 years ago
- Synteny Imager☆62Updated 8 months ago
- A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies☆59Updated 5 years ago
- This repository houses the code to run SURPI+, a rapid computational pipeline for comprehensive identification of pathogens from clinical…☆40Updated 5 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆72Updated 5 years ago
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆18Updated 4 years ago
- Improve the quality of a denovo assembly by scaffolding and gap filling☆57Updated 4 years ago
- Automates running of OrthoMCL software from http://orthomcl.org/common/downloads/software/v2.0/☆80Updated 4 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆57Updated last year
- Tools for working with second gen assemblies, fasta sequences, etc☆93Updated 8 years ago
- SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organism…☆59Updated 2 years ago
- Lima - Demultiplex Barcoded PacBio Samples☆66Updated last week