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2021_bioinformatics_fellowship

Project 2 Resources

abricate

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

bioconda-recipes

Conda recipes for the bioconda channel.

cfml-maskrc

Masks recombinant regions in an alignment based on ClonalFrameML output

clustcompare

Pipeline to compare secondary metabolite biosynthetic gene clusters (BGCs)

ekidna

Assembly based core genome SNP alignments for bacteria

fastkaptive

gcluster

A simple-to-use tool for visualizing and comparing genome contexts for numerous genomes

genbank_submit

Scripts and instructions for submitting annotated microbial genomes to Genbank

ggmsa

:traffic_light: Visualizing publication-quality multiple sequence alignment using ggplot2

intranet-crawler

Crawls a website

isfinder_database

download isfinder database

kleborate

magpurify

Improvement of metagenome-assembled genomes

make_prokka_db

A script for downloading complete sequences from genbank and make blast database for use with prokka

metaerg

metagenomics

Scripts for metagenomics and next generation sequencing data analysis

metagenomics_basic

Basic analysis of metagenomics from assembly to gene abundance

metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

metawrap

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

microbecensus

MicrobeCensus estimates the average genome size of microbial communities from metagenomic data

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

orthofinder

Phylogenetic orthology inference for comparative genomics

p._stutzeri_complex_manuscript

Perlscripts used in this study

parallel-runner

Highly specialized parallel task runner that enforces good behavior.

perl_scripts_misc

Perl scripts written for projects, need to be better documented.

pgap

NCBI Prokaryotic Genome Annotation Pipeline

pirate

A toolbox for pangenome analysis and threshold evaluation.

pneumo-typer

Pneumo-Typer is a comprehensive prediction and visualization of serotype and sequence type for streptococcus pneumoniae using assembled genomes

pneumokity

PneumoKITy - Fast sensitive Pneumococcal Capsular Serotype screening from WGS data