genome-assembly

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

genome-annotation genome-assembly ltr-retrotransposons lai ltr-retriever

Updated Aug 6, 2020
Perl

mcveanlab / mccortex

Star

De novo genome assembly and multisample variant calling

genomics variant-calling kmer cortex genome-analysis genome-assembly de-bruijn-graphs genome-graph contigs

Updated Mar 28, 2019
C

lpryszcz / redundans

Star

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

python pipeline docker-image polymorphic gap closing fasta scaffolding assembled-contigs genome-assembly paired-end contigs heterozygous mate-pairs

Updated May 6, 2019
Perl

TheGeekiestOne / Coursera-Data-Structures-and-Algorithms-Specialization

Star

Master Algorithmic Programming Techniques. Learn algorithms through programming and advance your software engineering or data science career

computer-science algorithms cpp coursera programming-challenges learning-algorithms genome-assembly algorithms-and-data-structures algorithms-specialization shortest-paths-algorithms

Updated Dec 14, 2020
C++

vpc-ccg / haslr

Star

A fast tool for hybrid genome assembly of long and short reads

bioinformatics nanopore genomics pacbio genome-assembly long-reads hybrid-assembly

Updated Apr 22, 2020
C++

HingeAssembler / HINGE

Star

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"

genome-assembly

Updated Oct 15, 2020
C++

linzhi2013 / MitoZ

Star

MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes

genome-assembly mitochondrial mitochondrion mitoz

Updated May 12, 2021
Python

kishwarshafin / helen

Star

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

genomics genome-sequencing genomes oxford-nanopore genome-analysis genome-assembly genomic-data-analysis genome-scale-models human-genetics

Updated Oct 28, 2020
Python

BioJulia / GenomeGraphs.jl

Star

A modern genomics framework for julia

bioinformatics genomics biology julia bio genome-sequencing genomes genome-assembly genome-graph bioinformatics-analysis

Updated Jul 6, 2020
Julia

tanghaibao / allhic

Star

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

golang pipeline genomics genetic-algorithm hi-c genome-assembly genome-scaffolding contigs polyploid heterozygous lachesis inter-contig-links

Updated May 24, 2021
Jupyter Notebook

bcgsc / tigmint

Star

⛓ Correct misassemblies using linked AND long reads

bioinformatics genome-assembly genome-scaffolding 10xgenomics misassembly-correction linked-reads bioinformatics-tool

Updated Sep 2, 2021
C++

brentp / indelope

Sponsor Star

find large indels (in the blind spot between GATK/freebayes and SV callers)

genomics vcf variant-calling k-mer-counting genome-assembly nim-lang local-assembly

Updated Dec 3, 2017
Nim

jteutenberg / downpore

Star

Suite of tools for use in genome assembly and consensus. Work in progress.

long-read genome-assembly genome-scaffolding genome-mapping

Updated Mar 22, 2021
Go

nf-core / bacass

Star

Simple bacterial assembly and annotation pipeline

workflow nanopore pipeline nextflow assembly denovo genome-assembly denovo-assembly bacterial-genomes nanopore-sequencing nf-core hybrid-assembly

Updated Aug 28, 2021
Nextflow

koszullab / instaGRAAL

Star

Large genome reassembly based on Hi-C data, continuation of GRAAL

genomics hi-c scaffolding 3c genome-assembly

Updated May 10, 2021
Cuda

NCBI-Hackathons / ViruSpy

Star

A pipeline for viral identification from metagenomic samples

virus metagenomics genome-assembly viral sra virus-integration virus-discovery viral-contigs

Updated Oct 15, 2017
Shell

ganlab / GALA

Star

Long-reads Gap-free Chromosome-scale Assembler

nanopore pacbio scaffolding genome-analysis genome-assembly long-reads gap-filling

Updated Aug 11, 2021
Python

yjx1217 / LRSDAY

Star

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

genomics genome-annotation oxford-nanopore genome-assembly yeast pacbio-data yeastgenome

Updated Jan 10, 2021
Shell

seryrzu / centroFlye

Star

An algorithm for centromere assembly using long error-prone reads

genomics genome-assembly long-reads long-read-sequencing centromere

Updated May 25, 2021
Python

marbl / MetagenomeScope

Star

Web visualization tool for (meta)genome assembly graphs

visualization metagenomics genome-assembly

Updated Feb 19, 2021
JavaScript

adigenova / fast-sg

Star

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

nanopore pacbio scaffolding illumina genome-assembly hybrid-genome-assembly alignment-free-algorithm

Updated May 29, 2018
C++

compbiol / CAMSA

Star

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

python genomics comparative-genomics genome-assembly genome-scaffolding scaffold-assembly asssembly-reconciliation

Updated Apr 13, 2020
Python

HuffordLab / NAM-genomes

Star

Detailed bioinformatics scripts and methods used in the NAM genome paper.

genomics genome-assembly bioinformatics-analysis bioinformatics-scripts nam maize

Updated Sep 16, 2021
R

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