bogemad

mgt_scripts

Scripts to help in MGT scheme generation

gas

Basic annotation statistics for eukaryotic genomes

trycycler_scripts

Scripts for genome assembly with trycycler

integrity_checker

update_blast_db

genagr

Gene name grabber, grab fasta sequences from an annotated reference using gene names

CCMetagen

Microbiome classification pipeline

asqcan

Pipeline for bacterial genome assembly, quality control and annotation

theileria_orientalis_complete_genome_scripts

COG_gene_analysis

bohra

A pipeline for bioinformatics analysis of bacterial genomes

cervus_parse

A script for parsing zipped vcf files (from an Ion Torrent run) to a genotype format for Cervus

virseaqc

virseaqc - A combined pipeline for VIRal genome SEarching, Assembly, and Quality Control on Ion-Torrent instruments.

rucs_analysis

Collection of scripts for filtering and parse output from the RUCS pipeline

funannotate

Eukaryotic Genome Annotation Pipeline

snpiphy

An automated snp phylogeny pipeline

T_ori_genome_pipeline

Theileria varaint calling pipeline

maker_genome_annotation

Collection of python scripts for genome annotation with maker

nullarbor_it

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

marker_gene_phylogeny

Runs phylosift to generate a marker gene phylogeny, useful for intra-genus comparisons.

snp_phylogeny

A pipeline for running SNP-based phylogenetic analysis

bioconda-recipes

Conda recipes for the bioconda channel.

analysis_template

Starting point for a conda-based analysis folder

bact_vcp

Another variant calling pipeline