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audioreactiveled

bioinfo-tools

Repo of scripts I use(d) for various tasks

bwise

de Bruijn Workflow using Integral information of Short pair End reads

cash

Compare and shuffle heterozygosity using BED and VCF files

circosalignmentplotter

Converts a part of an alignment (.PAF perhaps others sometimes) to a Circos image using BED and fasta files.

cocoa

Coverage Of COntigs Alignment

dotplot

Produce .svg dotplot from .paf alignement

genome_evolution_bdelloids_scripts

hap_phase

Phase haplotypes from at least n samples using HapCut2 and a VCF

happy

Haploidy and Size Completeness Estimation

hilma

Hilbert Mapper is a C++ implementation of Hilbert's space filling curve to represent read coverage on genomic sequences. Although it can be used to represent any unidimensional vector of positive numerical data.

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

mstrthss

plastz

Parallel Lastz

playassembly

Test assembly

pride

PriDe: Primer Design tool

prp

rungatk

Small GATK alignment and variant calling pipeline using python

savi

Simple Alignment Viewer

seqan2.4.0

Copy of seqan

strip

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