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    92 repositories

    • gff_diff

      Public
      A tool to generate a JSON diff between two GFF files, written in Rust
      Rust
      •1•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • sanger-pathogens.github.io

      Public
      Summary of Sanger Pathogen's Repos
      Python
      •2•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • update_pipeline

      Public
      Update a pipelines metadata
      Perl
      •
      Other
      •14•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • gffmunger

      Public
      Munges GFF3 files exported from Chado (http://www.gmod.org/) database to make them suitable for loading into WebApollo.
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • Bio-VertRes-Config

      Public
      Perl
      •
      Other
      •9•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • Bio-Path-Find

      Public
      Perl
      •
      Other
      •5•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • companion

      Public
      Pipeline for automatic eukaryotic parasite annotation
      Lua
      •
      ISC License
      •19•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • Fastaq

      Public
      Python3 scripts to manipulate FASTA and FASTQ files
      Python
      •
      Other
      •21•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • Farm_blast

      Public
      Python3 module to run blast+ or blastall in parallel on an LSF compute farm
      Python
      •
      Other
      •5•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • Bio-RNASeq

      Public
      The new Sanger Pathogen Informatics RNA Seq analysis pipeline
      Perl
      •
      Other
      •10•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • Bio-PacbioMethylation

      Public
      Runs Pacbio methylation pipeline
      Perl
      •
      Other
      •2•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • Bio-ReferenceManager

      Public
      Perl
      •
      Other
      •2•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • assembly_improvement

      Public
      Improve the quality of a denovo assembly by scaffolding and gap filling
      Perl
      •
      Other
      •21•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • saffrontree

      Public
      SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
      Python
      •
      Other
      •4•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • vr-codebase

      Public
      The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute
      Perl
      •
      Other
      •34•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • PySnpSites

      Public
      Experiments optimising python (with Cython)
      Python
      •3•0•0•0•Updated Jul 22, 2022Jul 22, 2022

    • Bio-Metagenomics

      Public
      Perl
      •
      Other
      •4•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • Bio-InterProScanWrapper

      Public
      Perl
      •
      Other
      •7•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • Bio-AutomatedAnnotation

      Public
      Perl module to take in an genomic assembly and produce annoation
      Perl
      •
      Other
      •8•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • plasmidtron

      Public
      Assembling the cause of phenotypes and genotypes from NGS data
      Python
      •
      Other
      •8•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • iva

      Public
      de novo virus assembler of Illumina paired reads
      Python
      •
      Other
      •19•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • Artemis

      Public
      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
      •
      Other
      •77•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • GeneDB-static

      Public
      Static version of GeneDB website
      HTML
      •
      Other
      •3•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • assembly-stats

      Public
      Get assembly statistics from FASTA and FASTQ files
      C++
      •
      Other
      •23•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • Bio-ENA-DataSubmission

      Public
      Perl
      •
      Other
      •8•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • circlator

      Public
      A tool to circularize genome assemblies
      Python
      •
      Other
      •60•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • ntd_website

      Public
      Wellcome Sanger Institute NTD website
      JavaScript
      •
      Other
      •2•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • snp-sites

      Public
      Finds SNP sites from a multi-FASTA alignment file
      C
      •
      Other
      •50•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • mlst_check

      Public
      Multilocus sequence typing by blast using the schemes from PubMLST
      Perl
      •
      Other
      •16•0•0•0•Updated Jul 21, 2022Jul 21, 2022

    • remove_blocks_from_aln

      Public
      Python
      •
      Other
      •7•0•0•0•Updated Jul 21, 2022Jul 21, 2022