raymondkiu
Research Fellow | Microbial Genomics | Metagenomics | Transcriptomics | R | Bash | Unix Shell | AWK
Institute of Microbiology and Infection, University of BirminghamUK
Pinned Repositories
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
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
eggnog-mapper_COGextraction
Extraction of COG functional classes and save the data in csv format
fastq-info
Calculate fastq reads and sequencing coverage
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.
R-scripts-graphing-statistics
My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq
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.
raymondkiu's Repositories
raymondkiu/bioinformatics-tools
Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files
raymondkiu/fastq-info
Calculate fastq reads and sequencing coverage
raymondkiu/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.
raymondkiu/R-scripts-graphing-statistics
My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq
raymondkiu/bactspeciesID
Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies
raymondkiu/bracken-filter-reads
This script filters low abundant reads from Bracken outputs for downstream analyses
raymondkiu/binary_tree
To convert gene-presence-absence matrix into multi fasta alignment
raymondkiu/eggnog-mapper_COGextraction
Extraction of COG functional classes and save the data in csv format
raymondkiu/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.
raymondkiu/16S_extraction_Barrnap
Automated 16S sequence extraction using Barrnap output gff files
raymondkiu/fastq_reads
Count fastq reads
raymondkiu/Genome-extraction-metagenome
Extracting single genome from a complex metagenome using reference based approaches
raymondkiu/Infant-Clostridium-perfringens-Paper
Source data files and sequence databases used in the paper
raymondkiu/Plotting
R scripts for routine plotting tasks
raymondkiu/R-stats
Statistical testing using R packages - various examples great for R beginners.
raymondkiu/TOXIper
Toxinotype assignment of Clostridium perfringens via ABRicate
raymondkiu/Bifidobacterium-IEC-transcriptomics
Codes used to analyse RNA-Seq data
raymondkiu/cfml-maskrc
Masks recombinant regions in an alignment based on ClonalFrameML output
raymondkiu/databases
My personal sequence databases
raymondkiu/Food-poisoning
raymondkiu/genomesizebp_fasta
Compute genome size of fasta assemblies
raymondkiu/Infant-Resistome-Study
Source data files (also R scripts) used in the paper
raymondkiu/Maternal-foetal-microbiota-paper
Scripts for differential gene expression analysis
raymondkiu/meanPhredScore
raymondkiu/printProkkaStats
Print a table of Prokka annotation stats (output .txt)
raymondkiu/raymondkiu.github.io
My website
raymondkiu/reference
raymondkiu/reverse_complement_nucleotide
To compute reverse complement of nucleotide sequences
raymondkiu/Thesis
Data generated in my thesis in 2018
raymondkiu/vertical_horizontal
To convert vertical text into horizontal text with spacing in between.