genopaths-africa Goto Github PK

abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

filtlong

quality filtering tool for long reads

flye

De novo assembler for single molecule sequencing reads using repeat graphs

genopaths-api

GenoPaths API - REST API Server for GenoPaths Platform

genopaths-charts

Bio-informatics data visualization and analysis graphs

genopaths-desktop

GenoPaths Desktop - Desktop Client for GenoPaths Platform

genopaths-icons

Bio-informatics icons

genopaths-platform

GenoPaths Platform

genopaths-web

GenoPaths Web - GenoPaths Web Client

genopaths-worker

GenoPaths Job Executor

hamronization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

ideel

Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes

kleborate

medaka

Sequence correction provided by ONT Research

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

mlst

:id: Scan contig files against PubMLST typing schemes

mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

nanoplot

Plotting scripts for long read sequencing data

newick-tools

Visualize and perform a multitude of operations on newick files

phylotree.js

Interactive viewer of phylogenetic trees

pilon

Pilon is an automated genome assembly improvement and variant detection tool

plasmidseeker

A k-mer based program for the identification of known plasmids from whole-genome sequencing reads

portal

Canadian VirusSeq Data Portal

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

quast

Genome assembly evaluation tool

tetyper

transposable element typing pipeline

unicycler

hybrid assembly pipeline for bacterial genomes