mingjuhao Goto Github PK

abricate

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

any2fasta

Convert various sequence formats to FASTA

august-2019-consensus-accuracy-update

A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies

bac-genomics-scripts

Collection of scripts for bacterial genomics

bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

biomedical-knowledge-mining-book

:books: Biomedical knowledge mining using GOSemSim and clusterProfiler

cgview

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

ecoli_serotyping

In silico prediction of E. coli serotype

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

gaas

Genome Assembly and Annotation Service code

genericrepeatfinder

gephi

Gephi - The Open Graph Viz Platform

integron_finder

Bioinformatics tool to find integrons in bacterial genomes

kraken

Kraken taxonomic sequence classification system

mashtree

:deciduous_tree: Create a tree using Mash distances

medaka

Sequence correction provided by ONT Research

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

minipolish

A tool for Racon polishing of miniasm assemblies

mlst

:id: Scan contig files against PubMLST typing schemes

pilon

Pilon is an automated genome assembly improvement and variant detection tool

plasme

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

python-random-quote

A file-based quote bot written in Python

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:

racon-1

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

raven

De novo genome assembler for long uncorrected reads

rebaler

reference-based long read assemblies of bacterial genomes

shovill

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads