PASSIONLab/ELBA

Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly

Language: C++ - Size: 106 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 12 - Forks: 8

holmrenser/IOGA

Iterative Organellar Genome Assembly

Language: Python - Size: 2.4 MB - Last synced: 2 months ago - Pushed: almost 4 years ago - Stars: 5 - Forks: 3

pommevilla/snakemake-genome-assembly-practice

Language: Python - Size: 125 KB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

yjx1217/LRSDAY

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Language: Perl - Size: 155 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 29 - Forks: 8

BeatsonLab-MicrobialGenomics/micropipe

A pipeline for high-quality bacterial genome construction using ONT sequencing

Language: HTML - Size: 57.4 MB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 36 - Forks: 9

chriskhalil/AbraracourcixMicroGenomeAssembler

Language: C++ - Size: 94.7 KB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

WileyBui/SARS-CoV-2-Assembled-Genome

Assembled & analyzed SARS-CoV-2 (Coronavirus) genome by using De Bruijn Graph.

Language: Python - Size: 19.8 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

ryought/dbgphmm

Probabilistic genome assembler based on de Bruijn Graph and profile HMM

Language: Rust - Size: 2.13 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

dominiquefastus/De-Novo-Genome-Sequencing-project

This is the working repository for the genome sequencing assembly. De-novo genome assembly and assessment.

Language: HTML - Size: 356 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

mcveanlab/mccortex

De novo genome assembly and multisample variant calling

Language: C - Size: 9.86 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 107 - Forks: 24

HuffordLab/Maize_NC358 Fork of oushujun/Maize_NC358

The repository for codes developed to generated the Maize NC358 assemblies and analyses.

Language: Jupyter Notebook - Size: 68.7 MB - Last synced: 2 months ago - Pushed: about 4 years ago - Stars: 10 - Forks: 4

tpoorten/compareAssemblies

Python script for comparing two genome assemblies

Language: Python - Size: 8.79 KB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 6 - Forks: 1

malonge/RaGOO

RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

Language: Python - Size: 143 KB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 162 - Forks: 28

tseemann/berokka

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

Language: Perl - Size: 3.51 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 24 - Forks: 4

shelkmike/Elloreas

Elloreas, a genome assembler

Language: Perl - Size: 915 KB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

seryrzu/centroFlye 📦

An algorithm for centromere assembly using long error-prone reads

Language: Python - Size: 4.82 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 25 - Forks: 5

roblehmann/compBio2021

Teaching Material for Course "Computational Bioscience & Machine Learning 2021 - Genome Assembly"

Language: Shell - Size: 186 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 4 - Forks: 1

HMPNK/CSA2.6

Chromosome Scale Assembler: A high-throughput chromosome scale genome assembly pipeline for vertebrate genomes

Language: Perl - Size: 1.52 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 10 - Forks: 6

HKU-BAL/CONNET

CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning

Language: Python - Size: 15.3 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 11 - Forks: 5

HingeAssembler/HINGE 📦

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

Language: C++ - Size: 5.9 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 64 - Forks: 9

hackseq/modular-assembly-hs18

Mix and match modular genome assembler components

Language: Makefile - Size: 98.6 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 8 - Forks: 9

holsapple/BUSCO-with-BLASTp

an attempt to incorporate BLASTp into BUSCO

Language: Python - Size: 1.56 MB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 1 - Forks: 1

raymondkiu/sequence-stats

Generate statistics from FASTQ and FASTA files. Also manipulate sequences such as renaming contigs and converting FASTQ to FASTA. Written in Bash. All in one place.

Language: Shell - Size: 87.9 KB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 6 - Forks: 0

raymondkiu/bactspeciesID

Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

Language: Shell - Size: 77.1 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 2

holsapple/Trinity-analysis

an investigation into the efficiency of Trinity transcriptome assemblies

Language: Python - Size: 4.88 KB - Last synced: 8 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

rorycraig337/Chlamydomonas_comparative_genomics

Language: Perl - Size: 7.64 MB - Last synced: 8 months ago - Pushed: about 4 years ago - Stars: 4 - Forks: 4

c0d3rb4b4/assembly-converter

A utility to convert chromosome coordinates between different assemblies.

Language: Perl - Size: 24.4 KB - Last synced: 8 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

ReemaSingh/Gen2Epi

A pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes.

Language: Perl - Size: 868 KB - Last synced: 8 months ago - Pushed: over 3 years ago - Stars: 3 - Forks: 0

lyy005/Aphid_AL4_chromosome_assembly

The analytical pipeline of the AL4 strain genome

Language: R - Size: 1.01 MB - Last synced: 8 months ago - Pushed: over 4 years ago - Stars: 2 - Forks: 4

orangeSi/Grainbow

show the genome structure variation or assembly error by pair-end or mate-pair reads

Language: Perl - Size: 6.1 MB - Last synced: 8 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

agudeloromero/EVEREST 📦

Viral genome assemble and characterisation

Language: Python - Size: 79.1 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 9 - Forks: 0

DenisVerkhoturov/geney

De Bruijn graph-based De Novo genome assembly CLI tool

Language: Scala - Size: 221 KB - Last synced: 8 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 3

tanghaibao/allhic

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

Language: Jupyter Notebook - Size: 28.6 MB - Last synced: 7 months ago - Pushed: about 3 years ago - Stars: 56 - Forks: 11

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

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

Language: C++ - Size: 18 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 145 - Forks: 65

gFedonin/VirGenA

A reference guided assembler of highly variable viral genomes

Language: Java - Size: 843 KB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 7 - Forks: 2

Sarah-Hesham-2022/De-Bruijn-Graph-for-Genome-Assembly

Data Analysis for Genomics, De Bruijn Graph for Genome Assembly.

Language: Python - Size: 230 KB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 1 - Forks: 0

dawelab/Ab10-Assembly

B73Ab10 genome assembly methods

Language: Python - Size: 668 KB - Last synced: 3 months ago - Pushed: over 2 years ago - Stars: 15 - Forks: 6

vpc-ccg/haslr

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

Language: C++ - Size: 155 KB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 73 - Forks: 9

broadinstitute/viral-ngs

Viral genomics analysis pipelines

Language: Python - Size: 64.5 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 180 - Forks: 66

wtsi-hpag/AncesBin

Pipeline to bin 10X, HiC, PacBio and ONT reads based on ancestry assemblies

Language: C - Size: 3.18 MB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

fabio-cunial/pav-wdl Fork of broadinstitute/pav-wdl

Runs several variant callers that align an assembly to a reference

Language: wdl - Size: 9.12 MB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

iomyaki/Anopheles-assembly

Language: Python - Size: 1.95 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

kishwarshafin/helen

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

Language: Python - Size: 7.27 MB - Last synced: 21 days ago - Pushed: over 3 years ago - Stars: 68 - Forks: 9

Sarah-Hesham-2022/De-Bruijn-Graph-Chain-Merging-Compacting

Data Analysis for Genomics, De Bruijn Graph Chain Merging Compacting.

Language: Python - Size: 393 KB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

Sarah-Hesham-2022/Euler-Path-for-Genome-Assembly

Data Analysis for Genomics, Euler Path for Genome Assembly.

Language: Python - Size: 2.93 KB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

sachanganesh/velour

parallel de novo genome assembler

Language: Go - Size: 146 KB - Last synced: 10 months ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 0

HUMANIAM/Algorithms_DataStructure_Specialization

this is repo about my solutions of problems in Data Structures and Algorithms Specialization in coursera site from algorithmic toolbox to Genome Assembly Programming Challenge

Language: C++ - Size: 36.5 MB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 8 - Forks: 2

ganlab/GALA

Long-reads Gap-free Chromosome-scale Assembler

Language: Python - Size: 4.87 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 60 - Forks: 12

rikuu/kermit

guided genome assembler using colored overlap graphs

Language: C - Size: 235 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 7 - Forks: 3

ratulSharker/Havec

An efficient approach for constructing de-bruijn graph for genome assembly

Language: C++ - Size: 264 KB - Last synced: 10 months ago - Pushed: almost 7 years ago - Stars: 3 - Forks: 0

weng-lab/cabbagelooper

Cabbage looper

Language: CSS - Size: 101 KB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 2 - Forks: 1

HingeAssembler/hingeassembler.github.io

HINGE website

Language: CSS - Size: 708 KB - Last synced: 10 months ago - Pushed: about 7 years ago - Stars: 2 - Forks: 1

HaFred/parallel_smith_waterman

A Series of SW Parallelization for Genome Assemblies

Language: Cuda - Size: 1.01 MB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

roblehmann/hts_workshop2019_genomics

Genomics Part of the KAUST High Throughput Sequencing Workshop 2019

Language: Shell - Size: 187 MB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 1

roblehmann/hts_workshop2019

Hands-on Introduction to Data Analysis for Genomics and Transcriptomics

Size: 76.6 MB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 1

acvill/nodeSeqs

Shell script for extracting sequences from high-degree nodes in metagenomic assembly graphs

Language: Shell - Size: 76.1 MB - Last synced: 10 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

rishavray/agent

Lift same species genome co-ordinates from one assembly to another

Language: Python - Size: 4.06 MB - Last synced: 10 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

algbio/practical-omnitigs

A repository to conduct experiments with omnitig-related models for genome assembly.

Language: Jupyter Notebook - Size: 4.44 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 3 - Forks: 0

Kareem-Mohamed-Wardany/Paired-Reads-Assemble

Paired Reads Assembly

Language: Python - Size: 86.9 KB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

ban-m/jtk

JTK -- a regional diploid genome assembler

Language: Rust - Size: 5.54 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 18 - Forks: 1

wurmlab/genomicscourse

For QMUL's Genome Bioinformatics MSc module BIO721P & SIB's Spring school in bioinfo & population genomics

Language: HTML - Size: 1.31 GB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 11 - Forks: 19

viadanna/GeneticAssembler

A Genome assembler based on greedy and genetic algorithms written in Go [golang.org]

Language: Python - Size: 4.28 MB - Last synced: 11 months ago - Pushed: almost 9 years ago - Stars: 0 - Forks: 1

EverymanBio/pestalotiopsis

Assembly and phylogentic analysis pipeline for draft genome of a Pestalotiopsis fungi.

Language: Python - Size: 205 KB - Last synced: 4 months ago - Pushed: about 2 years ago - Stars: 7 - Forks: 2

xjtu-omics/ChineseQuartetGenome

Genome assembly and variant benchmarks for Chinese Quartet

Language: Python - Size: 60.8 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 0

weigelworld/auto-asm

snakemake long read assembly pipeline

Language: Python - Size: 43 KB - Last synced: 9 months ago - Pushed: almost 5 years ago - Stars: 4 - Forks: 4

merlyescalona/yagcloser

YAGCloser: Yet-Another-Gap-Closer based on spanning of long reads.

Language: Python - Size: 85 KB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 0

ScarletBlizzard/YADeNA

Yet Another De Novo Assembler (Work in progress)

Language: Python - Size: 345 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 2

NCBI-Hackathons/ViruSpy

A pipeline for viral identification from metagenomic samples

Language: Shell - Size: 8.68 MB - Last synced: about 2 months ago - Pushed: over 6 years ago - Stars: 25 - Forks: 4

jteutenberg/downpore

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

Language: Go - Size: 332 KB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 31 - Forks: 0

Rowena-h/FusariumLifestyles

Scripts for Hill et al. (2022) doi:10.1093/molbev/msac085

Language: R - Size: 19.4 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 3 - Forks: 3

bcgsc/physlr

:chains: Construct a Physical Map from Linked Reads

Language: Python - Size: 2.17 MB - Last synced: 16 days ago - Pushed: about 2 months ago - Stars: 15 - Forks: 7

Rowena-h/EndophyteGenomes

Scripts for Hill et al. (2023) doi:10.1093/gbe/evad038

Language: Shell - Size: 2.68 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

bcgsc/ABySS-explorer

Visualize genome sequence assemblies

Language: Java - Size: 220 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 6 - Forks: 0

mariachiaragrieco/prunus-cp-genome-assembly

Assembly of chloroplast genome using long-reads and short-reads for Genomics Course 2021 (MSc Bioinformatics for Computational Genomics)

Language: Shell - Size: 10.7 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

nf-core/vipr 📦

Assembly and intrahost / low-frequency variant calling for viral samples

Language: Nextflow - Size: 217 KB - Last synced: 4 months ago - Pushed: over 4 years ago - Stars: 14 - Forks: 10

svpipaliya/de-novo-genome-assembly

Scripts for genome assembly associated tasks - scripts and parameters set up for run on Compute Canada HPC

Language: R - Size: 11 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

DenisVerkhoturov/metamer

Genome assembler de novo that uses De Bruijn graph.

Language: Java - Size: 262 KB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 2 - Forks: 5

ayixon/genomescanner

Experimental tool to taxonomically classify microbial genomes in a few minutes

Language: Shell - Size: 62.5 KB - Last synced: 4 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

sagnikbanerjee15/fungal_genome_assemblies_and_annotation

Analysis workflow to generate fungal assemblies, generate gene structural and functional annotations

Language: Shell - Size: 1.11 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 3 - Forks: 0

jnarayan81/setu

SARS-CoV-2 Genome Assembler

Language: Shell - Size: 33.5 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 12 - Forks: 1

fedarko/MetagenomeScope 📦

Hierarchical scaffold/assembly graph web visualization tool. As of August 9, 2017, the official repository for this has moved to MarBL! Use that repository instead :)

Language: Python - Size: 38.4 MB - Last synced: 12 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

stefankusch/genome_Myriosclerotinia_2020 📦

Genome assembly (short and long read) and quality control.

Size: 114 KB - Last synced: 11 days ago - Pushed: about 4 years ago - Stars: 1 - Forks: 3

a-ludi/dentist-example 📦

A small example to test DENTIST's workflow

Language: Python - Size: 127 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

Kareem-Mohamed-Wardany/Single-Reads-Assemble

Single Reads Assembly

Language: Python - Size: 5.86 KB - Last synced: 6 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

moozeq/tsg2-figassembly

Fasta reads assembly tool

Language: Python - Size: 7.81 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

navjindervirdee/Genome-Sequencing

Assembled Phi-X174 genome using Overlap Graph, Kmer Composition and De-Bruijn Graph.

Language: Java - Size: 16.6 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 8 - Forks: 3

wanyuac/geneDetector Fork of rrwick/SRST2-table-from-assemblies 📦

A tool for conducting a gene screen on assemblies, producing an SRST2-like output.

Language: Python - Size: 72.3 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

hunglin59638/makura

NCBI Genome downloader

Language: Python - Size: 143 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

Abusagit/BODBuilder

Basic-Operational De-Bruijn graph Builder (BODBuilder) is automatic program building De-Bruijn graph from given set of sequences. Self-pruning builder and errors estimator.

Language: Python - Size: 29.3 KB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

gwct/referee

Reference genome quality scores

Language: Python - Size: 88.3 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 18 - Forks: 3

nicolo-tellini/LRSDAY-Patch

Patch for LRSDAY v1.6 for Debian-based and SUSE-based OS.

Language: Shell - Size: 1.33 MB - Last synced: 4 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

darcyabjones/mitoflow

A small pipeline for assembling mitochondrial genomes and filtering reads prior to assembly.

Language: Groovy - Size: 36.1 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 6 - Forks: 1

escasinas/nanogap

A long read nanopore genome assembly and error correction pipeline

Language: Python - Size: 37.1 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

charlesfoster/mitowrap

A snakemake pipeline wrapping MitoZ and getOrganelle for de novo mitogenome assembly using short reads and subsequent QC.

Language: Python - Size: 10.7 KB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

avera1988/Genome_Assembly_lecture

A lecture for basic genome assembly

Language: Perl - Size: 21.8 MB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 2

wangyibin/collapse_rescue

Method for rescuing collapsed contigs.

Language: Python - Size: 10.7 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

zyxue/vr2c

Visualize read-to-contig alignment during assembly analysis

Language: Python - Size: 66.4 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 2 - Forks: 0

hoytpr/Lacto_genome

Progress on the Lactococcus strain PrHT3

Language: CSS - Size: 2.49 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

adigenova/fast-sg

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

Language: C++ - Size: 14.7 MB - Last synced: 7 months ago - Pushed: about 6 years ago - Stars: 22 - Forks: 3

katarinastuart/Sv3_StarlingGenome

Scripts and notes related to the manuscript: Stuart KC & Edwards RJ et al. 2022. Transcript- and annotation-guided genome assembly of the European starling. Molecular Ecology Resources, doi.org/10.1101/2021.04.07.438753. † joint first author

Language: Shell - Size: 32.8 MB - Last synced: 12 months ago - Pushed: almost 2 years ago - Stars: 3 - Forks: 0