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  sanger-pathogens

  Joined on Feb 2, 2015

12 projects

ariba

Last released on Feb 26, 2018

ARIBA: Antibiotic Resistance Identification By Assembly

pyfastaq

Last released on Feb 19, 2018

Script to manipulate FASTA and FASTQ files, plus API for developers

circlator

Last released on Jan 31, 2018

circlator: a tool to circularise genome assemblies

iva

Last released on Jan 25, 2018

Iterative Virus Assembler

seroba

Last released on Nov 21, 2017

SEROBA: Serotyping for illumina reads

pymummer

Last released on Aug 21, 2017

Wrapper for MUMmer

farmpy

Last released on Aug 11, 2017

Package to run farm jobs - currently LSF supported

bio_assembly_refinement

Last released on Apr 19, 2016

Assembly refinement tools, mostly useful for (but not limited to) pacbio bacterial assemblies

jsontoemail

Last released on Mar 28, 2015

Deprecated: please use json2email instead

json2email

Last released on Mar 28, 2015

Takes a jinja2 template and some json and sends an email

path_pipe_conf_tools

Last released on Mar 26, 2015

Tools for working with the pathogen pipeline at The Wellcome Trust Sanger Institute

farm_blast

Last released on Feb 2, 2015

Package to run blast in parallel on a compute farm

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