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gene-puller Public
Reworked version of Torsten Seemann's gene-puller.pl script. Retrieves aligned gene sequences from assemblies.
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genome-map Public
Draw genome coverage map
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mlst-cc Public
Identifies similar MLST profiles from the same clonal complex
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kraken-extract Public
Extract sequences classified as specified taxa
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fastablasta Public
Python blastn wrapper
Python GNU General Public License v2.0 UpdatedJul 23, 2019 -
maskrc-svg Public
Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
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pilon-correct Public
Corrects PacBio assemblies using Illumina short-reads
Shell GNU General Public License v3.0 UpdatedNov 8, 2018 -
extract_core_snps Public
Extracts core SNPs from a metagenome for strain-level resolution
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roary2fripan Public
Formats Roary output for viewing in FriPan
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fa-reverse Public
Reverse complement FASTA sequence
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fa-mask Public
Masks specified regions in FASTA sequences
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cfml-maskrc Public
Masks recombinant regions in an alignment based on ClonalFrameML output
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contig-puller Public
Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence
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nullarbor-shovill Public
Runs nullarbor using shovill for assemblies
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ngamr Public
Detection of antimicrobial resistance (AMR) in Neisseria gonorrhoeae (NG)
UpdatedOct 26, 2017 -
fa-rename Public
Renames headers in FASTA file
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nw_scale-distances Public
Converts/scales distances in newick trees
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invariant-sites Public
Counts invariant/variant and masks variant sites from multi-FASTA alignment
Python GNU General Public License v3.0 UpdatedJun 13, 2017 -
afa-core Public
Generates lists of core/non-core sites from a multi-FASTA alignment for ClonalFrameML
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trim-aln Public
Performs basic alignment trimming
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nw_leafnames Public
Rename external nodes (leaves) in a newick tree
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mrods Public
Microbial Regions Of Difference / Synteny (RODS) - ABPHM17 Hackathon project
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sort-contigs Public
Sorts contigs in GENBANK or FASTA file
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ng23S-mutations Public
Identifies mutations in 1-4 copies of the 23S rRNA gene in Neisseria gonorrhoeae
Python GNU General Public License v3.0 UpdatedFeb 22, 2017 -
ngmaster Public
Forked from MDU-PHL/ngmasterIn silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
Python GNU General Public License v2.0 UpdatedJan 17, 2017 -
rename-reads Public
Creates symlinks to rename reads for either parsing to Nullarbor or for uploading to SRA/ENA
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fix-prokka-header Public
Fixes header in .gbk files generated by Prokka
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nullarbor-snippy-core Public
Runs snippy-core on a subset of isolates included in a Nullarbor run
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fq-plots Public
Estimates and displays read depth and insert size plots
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