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16s_extraction_barrnap

Automated 16S sequence extraction using Barrnap output gff files

bactspeciesid

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

bifidobacterium-iec-transcriptomics

Codes used to analyse RNA-Seq data

binary_tree

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

bioinformatics-tools

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

blastoutput2gff

Convert BLAST output (tabular format 6) to gff format for sequence extraction using bedtools

bracken-filter-reads

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

cfml-maskrc

Masks recombinant regions in an alignment based on ClonalFrameML output

databases

My personal sequence databases

eggnog-mapper_cogextraction

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

fastq-info

Calculate fastq reads and sequencing coverage

fastq_reads

Count fastq reads

food-poisoning

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.

genome-extraction-metagenome

Extracting single genome from a complex metagenome using reference based approaches

genomesizebp_fasta

Compute genome size of fasta assemblies

infant-clostridium-perfringens-paper

Source data files and sequence databases used in the paper

maternal-foetal-microbiota-paper

Scripts for differential gene expression analysis

meanphredscore

plotting

R scripts for routine plotting tasks

printprokkastats

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

r-scripts-graphing-statistics

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

r-stats

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

raymondkiu.github.io

My website

reference

reverse_complement_nucleotide

To compute reverse complement of nucleotide sequences

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.

thesis

Data generated in my thesis in 2018

toxiper

Toxinotype assignment of Clostridium perfringens via ABRicate

vertical_horizontal

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