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allhic

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

chrom3d

code_backup

deepgrp

DeepGRP is a package used to predict genomic repetitive elements.

edta

Extensive de-novo TE Annotator

gasal2

gatk

Official code repository for GATK versions 4 and up

gean

This toolkit deals with GEnomic sequence and genome structure ANnotation files between inbreeding lines and species.

hapcut2

software tools for haplotype assembly from sequence data

haphic

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

interproscan

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

juicebox

Visualization and analysis software for Hi-C data -

juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

lachesis

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)

loopextrusion

Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation

moms

A Multi-channel Optical Map Scaffolder

ngs_data_processing

Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.

note

pasapipeline

PASA software

pipeline

plann

Plann: a command-line application for annotating plastome sequences

potato_c88

Chromosome-scale and haplotype-resolved assmebly of tetraploid cultiavetd potato with polyploidy graph binning

smartie-sv

calling SVs from Blasr contig level alignments

telomeric-identifier

Identify and find telomeres, or telomeric repeats in a genome.

verkko

wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly