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

Source data files and sequence databases used in the paper

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.

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

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

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.

Scripts for differential gene expression analysis

Codes used to analyse RNA-Seq data

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

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

My personal sequence databases

Calculate fastq reads and sequencing coverage

Toxinotype assignment of Clostridium perfringens via ABRicate

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

Automated 16S sequence extraction using Barrnap output gff files

Data generated in my thesis in 2018

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

Extracting single genome from a complex metagenome using reference based approaches

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

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

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

Count fastq reads

Compute genome size of fasta assemblies