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rasusa
Randomly subsample sequencing reads or alignmentsssubmit
Submit slurm sbatch jobs without a scriptpafpy
A lightweight library for working with PAF (Pairwise mApping Format) filescompression_benchmark
Benchmarking FASTQ compression with 'mature' compression algorithmstaeper
A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.drprg
Drug Resistance Prediction with Reference Graphsnohuman
Remove human reads from a sequencing runontime
Extract subsets of ONT (Nanopore) reads based on timeskc
Shared k-mer content between two genomespsdm
Compute a pairwise SNP distance matrix from one or two alignment(s)container_recipes
Repository with all my container recipes π©βπ³streamformatics
Real-time species-typing visualisation for nanopore data.fast5seek
Subset of fast5 files contained in a fastq, BAM, or SAM file.tbpore
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing datapistis
Quality control plotting for long readsclassification_benchmark
Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and MTB classificationMemoryUnits
Python objects for dealing with metric units and memory, file, and genome sizes πΎreveal-hugo-nord
A nord-themed reveal-hugo presentation templatebioscripts
Collection of scripts for doing various taskshead_to_head_pipeline
Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.thesis
My PhD thesisrawmeth
Package for exploring raw signal of nanopore reads that have been resquiggled with nanoraw.eipp-2019-singularity
Singularity group project for EIPP 2019reveal-hugo-ebi
An EBI-themed reveal.js presentation template powered by reveal-hugoLongitude_pipeline
Pipeline for analysing M. tuberculosis nanopore reads and getting drug susceptibility information.Sepsis-methylation
Pipeline to analyse the dRNA methylation of sepsis samples.MTB_masks
A collection of genome masks for Mycobacterium tuberculosispandora_analysis_pipeline
cud
Color Universal Design colourblind-friendly python matplotlib palettetubemaps_pilot
Playing around with getting sequence tubemaps to work for population reference graphs.envs-primer
Presentation for EBI 2021 Predocs on software environments and containerstinysink
Synchronise Nanopore reads with a server.bam_slice
Cut slices out of a BAM file given a list of positions.Love Open Source and this site? Check out how you can help us