Raymond Kiu's Projects
Automated 16S sequence extraction using Barrnap output gff files
Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies
Codes used to analyse RNA-Seq data
To convert gene-presence-absence matrix into multi fasta alignment
Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files
Convert BLAST output (tabular format 6) to gff format for sequence extraction using bedtools
This script filters low abundant reads from Bracken outputs for downstream analyses
Masks recombinant regions in an alignment based on ClonalFrameML output
My personal sequence databases
Extraction of COG functional classes and save the data in csv format
Calculate fastq reads and sequencing coverage
Count fastq reads
fqtk: A toolkit to perform common tasks on FASTQ reads. Rename FASTQ identifiers, print FASTQ statistics and convert FASTQ to FASTA. This program is written in AWK and Bash.
Extracting single genome from a complex metagenome using reference based approaches
Compute genome size of fasta assemblies
Source data files and sequence databases used in the paper
Scripts for differential gene expression analysis
R scripts for routine plotting tasks
Print a table of Prokka annotation stats (output .txt)
My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq
Statistical testing using R packages - various examples great for R beginners.
My website
To compute reverse complement of nucleotide sequences
Generate statistics from FASTQ and FASTA files. Also manipulate sequences such as renaming contigs and converting FASTQ to FASTA. Written in Bash. All in one place.
Data generated in my thesis in 2018
Toxinotype assignment of Clostridium perfringens via ABRicate
To convert vertical text into horizontal text with spacing in between.