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Search results for assembly genome

205 search results found

Python library to facilitate genome assembly, annotation, and comparative genomics

A single molecule sequence assembler for genomes large and small.

Nanopolish ⭐ 496

Signal-level algorithms for MinION data

Hifiasm ⭐ 443

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Megahit ⭐ 442

Ultra-fast and memory-efficient (meta-)genome assembler

Unicycler ⭐ 428

hybrid assembly pipeline for bacterial genomes

Genome assembly evaluation tool

Tools for fast and flexible genome assembly scaffolding and improvement

Trycycler ⭐ 264

A tool for generating consensus long-read assemblies for bacterial genomes

Mashmap ⭐ 243

A fast approximate aligner for long DNA sequences

Merqury ⭐ 234

k-mer based assembly evaluation

Pyfastx ⭐ 211

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Getorganelle ⭐ 209

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)

Masurca ⭐ 207

Rapid comparison and dereplication of genomes

Soapdenovo2 ⭐ 197

Next generation sequencing reads de novo assembler.

Circlator ⭐ 193

A tool to circularize genome assemblies

Genome Assembly and Annotation Service code

Vgp Assembly ⭐ 160

VGP repository for the genome assembly working group

Rust Mdbg ⭐ 149

minimizer-space de Bruijn graphs (mdBG) for whole genome assembly

Nextpolish ⭐ 145

Fast and accurately polish the genome generated by long reads.

Novoplasty ⭐ 140

NOVOPlasty - The organelle assembler and heteroplasmy caller

Chromosome-level scaffolding using multiple references

Assemblytics ⭐ 124

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

Genome_updater ⭐ 123

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Shovill ⭐ 104

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

FunGAP: fungal Genome Annotation Pipeline

SKESA assembler

Genomewarp ⭐ 96

GenomeWarp translates genetic variants from one genome assembly version to another.

Peregrine ⭐ 94

Peregrine: Fast Genome Assembler Using SHIMMER Index

Sigprofilermatrixgenerator ⭐ 91

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

Mccortex ⭐ 86

De novo genome assembly and multisample variant calling

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

Genefuse ⭐ 86

Gene fusion detection and visualization

Opera Ms ⭐ 82

OPERA-MS - Hybrid Metagenomic Assembler

Same species annotation lift over pipeline.

Pb Assembly ⭐ 81

PacBio Assembly Tool Suite: Reads in ⇨ Assembly out

Nullarbor ⭐ 80

💾 📃 "Reads to report" for public health and clinical microbiology

A WGS de novo assembler based on the FMD-index for large genomes

Minia is a short-read assembler based on a de Bruijn graph

Ray -- Parallel genome assemblies for parallel DNA sequencing

The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

An accurate and ultra-fast hybrid genome assembler

Assembly Dereplicator ⭐ 57

A tool for removing redundant genomes from a set of assemblies

Jupiterplot ⭐ 54

A Circos-based tool to visualize genome assembly consistency

⛓ Correct misassemblies using linked AND long reads

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

Read Assembly and Annotation Pipeline Tool

Liftover ⭐ 51

liftover for python, made fast with cython

Appliedgenomics2017 ⭐ 49

JHU EN.600.649: Computational Genomics: Applied Comparative Genomics

a collection of scripts for organising bacterial genomes by species

Svim Asm ⭐ 48

Structural Variant Identification Method using Genome Assemblies

Pyliftover ⭐ 47

Pure-python implementation of UCSC liftOver genome coordinate conversion

A scalable bacterial genome assembly, annotation and analysis pipeline

Long-reads Gap-free Chromosome-scale Assembler

Fast Plast ⭐ 40

Automated de novo assembly of whole chloroplast genomes.

Blobology ⭐ 40

Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED)

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

Indelope ⭐ 39

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

August 2019 Consensus Accuracy Update ⭐ 39

A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies

Graph based multi genome aligner

Dnapipete ⭐ 38

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

Novograph ⭐ 36

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

Mitofinder ⭐ 32

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

all methods related to Enterobase

Fully automated generation of UCSC assembly hubs

reference-based long read assemblies of bacterial genomes

A fuzzy Bruijn graph approach to long noisy reads assembly

Mindthegap ⭐ 30

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

Tapestry ⭐ 29

Validate and edit small eukaryotic genome assemblies

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Metacompass ⭐ 26

MetaCompass: Reference-guided Assembly of Metagenomes

Vgp Tools ⭐ 26

Awesome Sequencing Tech Papers ⭐ 26

A collection of publications on comparison of high-throughput sequencing technologies.

Teloclip ⭐ 26

A tool for the recovery of unassembled telomeres from soft-clipped read alignments.

Organelle_pba ⭐ 23

A software to assemble chloroplast and mitochodrial genomes using PacBio data

Abbreviate strings to short, unique identifiers

Bioinformatics Course 2020 ⭐ 23

Order and orientation of complete bacterial genomes

Genelosspipe ⭐ 22

HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies

Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.

Score Assemblies ⭐ 20

Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)

Assembler Components ⭐ 20

Components of genome sequence assembly tools

Nanoflow ⭐ 20

🔬 De novo assembly of nanopore reads using nextflow

Scaff10x ⭐ 20

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Ratite Genomics ⭐ 19

Scripts and other material for the assembly and analysis of ratite genomes.

Assembly based core genome SNP alignments for bacteria

A list of weak Bacterial assemblies in GenBank

Mof Search ⭐ 18

BLAST-like search across all pre-2019 bacteria on ordinary laptop and desktop computers within a few hours

Sigprofilersimulator ⭐ 18

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

Seqsero2 ⭐ 18

Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.

⛓️ Construct a Physical Map from Linked Reads

Genome_collector ⭐ 17

🌠 Easily download genomes and build BLAST/Bowtie indexes in Python

Sigprofilermatrixgeneratorr ⭐ 17

R wrapper for utilizing the SigProfilerMatrixGenerator framework

Genome_assembly ⭐ 17

Om Hic Scaffolding ⭐ 17

Workflows for correcting and scaffolding long-read (PacBio, nanopore) genome assemblies using optical mapping and/or Dovetail Hi-C data

Economic Genome Assembly from Low Coverage Illumina and Nanopore Data

Bactpipe ⭐ 17

BACTpipe: An assembly and annotation pipeline for bacterial genomics

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