raymondkiu

bioinformatics-tools

Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files

fastq-info

Calculate fastq reads and sequencing coverage

sequence-stats

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.

R-scripts-graphing-statistics

My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq

bactspeciesID

Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

binary_tree

To convert gene-presence-absence matrix into multi fasta alignment

bracken-filter-reads

This script filters low abundant reads from Bracken outputs for downstream analyses

eggnog-mapper_COGextraction

Extraction of COG functional classes and save the data in csv format

fqtk

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.

16S_extraction_Barrnap

Automated 16S sequence extraction using Barrnap output gff files

fastq_reads

Count fastq reads

Genome-extraction-metagenome

Extracting single genome from a complex metagenome using reference based approaches

Infant-Clostridium-perfringens-Paper

Source data files and sequence databases used in the paper

Plotting

R scripts for routine plotting tasks

R-stats

Statistical testing using R packages - various examples great for R beginners.

TOXIper

Toxinotype assignment of Clostridium perfringens via ABRicate

Bifidobacterium-IEC-transcriptomics

Codes used to analyse RNA-Seq data

cfml-maskrc

Masks recombinant regions in an alignment based on ClonalFrameML output

databases

My personal sequence databases

Food-poisoning

genomesizebp_fasta

Compute genome size of fasta assemblies

Infant-Resistome-Study

Source data files (also R scripts) used in the paper

Maternal-foetal-microbiota-paper

Scripts for differential gene expression analysis

meanPhredScore

printProkkaStats

Print a table of Prokka annotation stats (output .txt)

raymondkiu.github.io

My website

reference

reverse_complement_nucleotide

To compute reverse complement of nucleotide sequences

Thesis

Data generated in my thesis in 2018

vertical_horizontal

To convert vertical text into horizontal text with spacing in between.