Name: Jason Kwong
Type: User
Company: Doherty Applied Microbial Genomics
Bio: Infectious Diseases Physician
& Early Career Research Fellow
Location: University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
Jason Kwong's Projects
Generates lists of core/non-core sites from a multi-FASTA alignment for ClonalFrameML
Masks recombinant regions in an alignment based on ClonalFrameML output
Extracts contigs harbouring a target gene / sequence from assemblies and aligns the contigs around the target sequence
Plots heatmap of SNPs
Extracts core SNPs from a metagenome for strain-level resolution
Masks specified regions in FASTA sequences
Renames headers in FASTA file
Reverse complement FASTA sequence
Python blastn wrapper
Fixes header in .gbk files generated by Prokka
Estimates and displays read depth and insert size plots
Reworked version of Torsten Seemann's gene-puller.pl script. Retrieves aligned gene sequences from assemblies.
Draw genome coverage map
Counts invariant/variant and masks variant sites from multi-FASTA alignment
Extract sequences classified as specified taxa
In silico serotype prediction for Listeria monocytogenes
Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG
Identifies similar MLST profiles from the same clonal complex
Microbial Regions Of Difference / Synteny (RODS) - ABPHM17 Hackathon project
Identifies mutations in 1-4 copies of the 23S rRNA gene in Neisseria gonorrhoeae
Detection of antimicrobial resistance (AMR) in Neisseria gonorrhoeae (NG)
In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST)
Runs nullarbor using shovill for assemblies
Runs snippy-core on a subset of isolates included in a Nullarbor run
Rename external nodes (leaves) in a newick tree
Resolves multifurcation / polytomy in Newick trees eg. from FastTree
Converts/scales distances in newick trees
Corrects PacBio assemblies using Illumina short-reads
Simple shell script to locate reads in a directory and format listing for various purposes
Creates symlinks to rename reads for either parsing to Nullarbor or for uploading to SRA/ENA