sanger-pathogens/Farmpy

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Created about 11 years ago
Updated over 5 years ago

sanger-pathogens/Farmpy

sanger-pathogens

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Python3 package to handle job submission to a compute farm

Roary

Rapid large-scale prokaryote pan genome analysis

circlator

A tool to circularize genome assemblies

Artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

snp-sites

Finds SNP sites from a multi-FASTA alignment file

ariba

Antimicrobial Resistance Identification By Assembly

assembly-stats

Get assembly statistics from FASTA and FASTQ files

Fastaq

Python3 scripts to manipulate FASTA and FASTQ files

pathogen-informatics-training

Jupyter Notebook

assembly_improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

iva

de novo virus assembler of Illumina paired reads

plasmidtron

Assembling the cause of phenotypes and genotypes from NGS data

gff3toembl

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

pymummer

Python3 module for running MUMmer and reading the output

mlst_check

Multilocus sequence typing by blast using the schemes from PubMLST

saffrontree

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Bio-Tradis

A set of tools to analyse the output from TraDIS analyses

companion

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

panito

Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment

nano-rave

Nextflow pipeline designed for rapid onsite QC and variant calling of Oxford Nanopore data (following basecalling and demultiplexing with Guppy).

Bio-RNASeq

The new Sanger Pathogen Informatics RNA Seq analysis pipeline

update_pipeline

Update a pipelines metadata

remove_blocks_from_aln

sanger-pathogens.github.io

Summary of Sanger Pathogen's Repos

SnpEffWrapper

Takes a VCF and applies annotations from a GFF using SnpEff

Bio-InterProScanWrapper

bact-gen-scripts

Bio-ENA-DataSubmission

mapping-and-snp-calling-training

Bio-PacbioMethylation

Runs Pacbio methylation pipeline

unix-training

A set of jupyter notebooks to provide unix training developed by Pathogen Informatics at Wellcome Sanger Institute.

Jupyter Notebook

Bio-Metagenomics

setup_tracking

setup a vrtracking pipeline

pipelines_reporting

baker

A tool to generate configuration files and wrapper scripts

chado-tools

Tools for accessing CHADO databases.

Bio-ReferenceManager

Bio-AutomatedAnnotation

Perl module to take in an genomic assembly and produce annoation

fastml

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

iva-publication

Supplementary scripts and data for the IVA publication

QC-training

PathFind-training

Jupyter Notebook

Farm_blast

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

assembly-and-annotation-training

singularity-bsub

Provides wrapper scripts for executing LSF commands within a Singularity container

monocle