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blaze

SingleCell Nanopore sequencing data analysis

bsmn-pipeline

BSMN common data processing pipeline

bumpversion

Commit the bumping of the version.py file

chopper

combine_images

Bit of Python code to resize and combine images

cramino

A *fast* tool for BAM/CRAM quality evaluation, intended for long reads

cutesv

Long read based human genomic structural variation detection with cuteSV

dea.r

Script to automate differential expression analysis using DESeq2, edgeR or limma-voom

determine-gender

Scripts to determine the gender of samples in exome and transcriptome sequencing

enrichr_cli

Python script to use enrichr from command line (http://amp.pharm.mssm.edu/Enrichr/)

exrede

expanded repeat detection from long reads

fast5purge

Purge a fast5 file from sensitive information

fastq-anonymous

Change the sequence of a fastq file to enable sharing of confidential information for troubleshooting

fastqmetrics

Extract metrics from a fastq file, streaming

germlinecnvcaller

Testing the GATK4.beta.5 GermlineCNVCaller

insurveyor

An insertion caller for Illumina paired-end WGS data.

kyber

make_arrow

A Rust tool to create an arrow file from a cram/bam file

methplotlib

Plotting tools for nanopore methylation data

minimap2-rs

mintie

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

misc

A mishmash of scripts written during my PhD

modkit

A bioinformatics tool for working with modified bases

nano-snakemake

A snakemake pipeline for SV analysis from nanopore genome sequencing

nanocomp

Comparison of multiple long read datasets

nanofilt

Filtering and trimming of long read sequencing data

nanoget

Functions to extract information from Oxford Nanopore sequencing data and alignments

nanogui

Graphical user interface for running nanoget

nanolive

Create live plots of a run using fast5 events

nanolyse

Remove lambda phage reads from a fastq file