pathogen-informatics Goto Github PK

bio-vertres-permissions

chado-export

A Python application for exporting organism sequences from a CHADO database to GFF file.

chado-tools

Tools for accessing CHADO databases.

circlator

A tool to circularize genome assemblies

citation_reporter

Website to show your team's publications (which are in PubMed)

companion

Pipeline for automatic eukaryotic parasite annotation

companion-publication

Accompanying information for the Companion publication

conda-recipes

Conda recipes for the sanger-pathogens channel: https://anaconda.org/sanger-pathogens

crawl2

A spiritual successor to Crawl

datapages

Static pages with convenient links to WTSI's pathogen sequencing data

deago

R package for generating HTML reports from differential expression analyis and GO term enrichment

deployment

external-import

Import external data into our tracking databases

farmpy

Python3 package to handle job submission to a compute farm

farm_blast

Python3 module to run blast+ or blastall in parallel on an LSF compute farm

fastaq

Python3 scripts to manipulate FASTA and FASTQ files

fasta_grep

Efficiently pull filter FASTA files

fastml

Addtional functionality for fastml, see http://fastml.tau.ac.il

fastqcheck

Generate statistics on and validate fastq files

find_files_for_deletion

genedb-static

Static version of GeneDB website

gff3toembl

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

gffmunger

Munges GFF3 files exported from Chado (http://www.gmod.org/) database to make them suitable for loading into WebApollo.

gff_diff

A tool to generate a JSON diff between two GFF files, written in Rust

githubconglomerate

Brings together details of github repos across organisations

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

hicf_checklist

iva

de novo virus assembler of Illumina paired reads

iva-publication

Supplementary scripts and data for the IVA publication

json2email

Takes a jinja2 template and some json and sends an email