tseemann Goto Github PK

2013-caltech-workshop

abricate

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

amplikate

📢🎯 Generic typing tool from amplicons and/or in silico PCR

angus

Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

anthrakks

Distinguish Bacillus cereus and biovar anthracis (anthrax)

any2fasta

Convert various sequence formats to FASTA

apc

(a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join

arborkart

Phylogenomic trees with maps for the web

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

asmngs18

ASMNGS18 - 2018 Conference Details

assembill

Simple script to clip, assemble, tile and annotate a bacterial genome from Illumina reads

atlas

atlas

babykraken

👶🦑 Very small Kraken2 database for bundling with pipelines

barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor

berokka

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

bioconda-recipes

Conda recipes for the bioconda channel.

bioinfo-scripts

Collection of bioinformatics utility scripts, mostly written in Bioperl

bng-tools

Useful post-processing scripts for BRATNextGen output data

bowkaster

cgMLST from FASTQ reads

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

canu

A single molecule sequence assembler for genomes large and small.

cdhit

Automatically exported from code.google.com/p/cdhit

cfml-maskrc

Masks recombinant regions in an alignment based on ClonalFrameML output

cgmlst-dists

🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables

clonalframeml

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

coginator

Assign COGs to protein sequences

cortex

reference free variant assembly

dehomopolymerate

Collapse sequence homopolymers to a single character

easy-web-blast

ekidna

Assembly based core genome SNP alignments for bacteria