charlesfoster Goto Github PK
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charlesfoster's Projects
bioconda-recipes
Conda recipes for the bioconda channel.
cmv_cerebral_organoid_paper
Code for CMV cerebral organoids paper
covid-illumina-snakemake
Pipeline written in snakemake to analyse SARS-CoV-2 Illumina data
deletion_detector
A simple program that uses parallel processing to detect deletions in fasta files relative to a reference genome.
filter_gaps_and_crap
A simple python script to filter out gappy/crappy sequences from a multiple sequence alignment.
mitowrap
A snakemake pipeline wrapping MitoZ and getOrganelle for de novo mitogenome assembly using short reads and subsequent QC.
ont-analysis-toolkit
A toolkit for monitoring ONT MinION sequencing, followed by data analysis, for viral genomes amplified with tiled amplicon sequencing.
pairwise_comparisons
A simple python3 program to compare aligned DNA/protein sequences.
parse_medaka_variants
Script to parse a vcf file from medaka variant calling and add read counts & allele frequency for the ALTs within. Beware of assumptions: check the README.
phd_thesis_supplementaryfiles
This repository contains the supplementary files referred to in my PhD thesis.
shiver
Sequences from HIV Easily Reconstructed
snipit
snipit: summarise snps relative to your reference sequence
useful_scripts
Scripts that have proved useful to me
vartracker
vartracker: track the persistence (or not) or mutations during longitudinal sequencing
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