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asgart

A genome-scale, fast, and precise segmental duplications mapping tool

bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

centromere_seeker

bash script to search for centromeric repeat patterns in PacBio data, using several current tools (trf and R)

deeptools

Tools to process and analyze deep sequencing data.

filtlong

quality filtering tool for long reads

finishingtool

finshingTool

foract

Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints

gff-rename

Replace sequence_IDs in gff3 based on given genome.fasta

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

long-read-genome-assembly

Genome assembly using ONT and PacBio data

longstitch

Correct and scaffold assemblies using long reads

masurca

mimeo

Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.

mpgap

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

nanome

NANOME(Nanopore methylation) pipeline of DNA methylation calling tools for Oxford Nanopore sequencing

ncbr_wgs_pipeline

nemadsq

A repository containing pipelines for nematode genome assembly, decontamination, scaffolding, and QC

ostracoda_genomes

Code for "First annotated draft genomes of non-marine ostracods (Ostracoda, Crustacea) with different reproductive modes" manuscript.

otipu_chrom_assem

Scripts and files associated with the chromosomal assembly of O. tipulae manuscript

peppi

Pipeline for protein-protein interaction prediction

phip-flow

A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets

pipeliner

Pipeliner Program

ragtag

Tools for fast and flexible genome assembly scaffolding and improvement

smansoni_genome

telomeric-identifier

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

trf2gff

Convert Tandem Repeat Finder dat file output into gff3 format