Discover sanger-pathogens/unix-training Open Source project

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sanger-pathogens

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

Roary

Rapid large-scale prokaryote pan genome analysis

Perl

317

circlator

A tool to circularize genome assemblies

Python

230

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

Java

217

snp-sites

Finds SNP sites from a multi-FASTA alignment file

215

ariba

Antimicrobial Resistance Identification By Assembly

Python

167

assembly-stats

Get assembly statistics from FASTA and FASTQ files

C++

115

Fastaq

Python3 scripts to manipulate FASTA and FASTQ files

Python

pathogen-informatics-training

Jupyter Notebook

assembly_improvement

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

Perl

iva

de novo virus assembler of Illumina paired reads

Python

plasmidtron

Assembling the cause of phenotypes and genotypes from NGS data

Python

gff3toembl

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

Python

pymummer

Python3 module for running MUMmer and reading the output

Python

mlst_check

Multilocus sequence typing by blast using the schemes from PubMLST

Perl

saffrontree

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

Python

Bio-Tradis

A set of tools to analyse the output from TraDIS analyses

Perl

companion

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Lua

seroba

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

Python

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).

Nextflow

Bio-RNASeq

The new Sanger Pathogen Informatics RNA Seq analysis pipeline

Perl

update_pipeline

Update a pipelines metadata

Perl

remove_blocks_from_aln

Python

Farmpy

Python3 package to handle job submission to a compute farm

Python

sanger-pathogens.github.io

Summary of Sanger Pathogen's Repos

Python

SnpEffWrapper

Takes a VCF and applies annotations from a GFF using SnpEff

Python

Bio-InterProScanWrapper

Perl

bact-gen-scripts

Python

Bio-ENA-DataSubmission

Perl

mapping-and-snp-calling-training

TeX

Bio-PacbioMethylation

Runs Pacbio methylation pipeline

Perl

Bio-Metagenomics

Perl

setup_tracking

setup a vrtracking pipeline

Perl

pipelines_reporting

Perl

baker

A tool to generate configuration files and wrapper scripts

Python

chado-tools

Tools for accessing CHADO databases.

Python

Bio-ReferenceManager

Perl

Bio-AutomatedAnnotation

Perl module to take in an genomic assembly and produce annoation

Perl

fastml

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

C++

iva-publication

Supplementary scripts and data for the IVA publication

Python

QC-training

Gnuplot

PathFind-training

Jupyter Notebook

Farm_blast

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

Python

assembly-and-annotation-training

TeX

singularity-bsub

Provides wrapper scripts for executing LSF commands within a Singularity container

Shell

monocle

Python

sanger-pathogens/unix-training

sanger-pathogens

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