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Search results for assembly genomics

54 search results found

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

Hifiasm ⭐ 443

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Megahit ⭐ 442

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

Hyena Dna ⭐ 379

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

Cellranger ⭐ 314

10x Genomics Single Cell Analysis

Miniasm ⭐ 195

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Circlator ⭐ 193

A tool to circularize genome assemblies

Antimicrobial Resistance Identification By Assembly

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

Redundans ⭐ 121

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

Bioinformatics library for .NET

Assembly Stats ⭐ 92

Get assembly statistics from FASTA and FASTQ files

Fermikit ⭐ 91

De novo assembly based variant calling pipeline for Illumina short reads

Wally: Visualization of aligned sequencing reads and contigs

Mccortex ⭐ 86

De novo genome assembly and multisample variant calling

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

Interactive assembly and analysis of RAD-seq data sets

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

A fork of minimap2 optimized for assembly-to-reference alignment

Appliedgenomics2017 ⭐ 49

JHU EN.600.649: Computational Genomics: Applied Comparative Genomics

Assembly_improvement ⭐ 39

Improve the quality of a denovo assembly by scaffolding and gap filling

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)

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).

GFA insert into GenomicSQLite

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.

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Awesome Sequencing Tech Papers ⭐ 26

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

Order and orientation of complete bacterial genomes

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.

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

Centroflye ⭐ 17

An algorithm for centromere assembly using long error-prone reads

Bactpipe ⭐ 17

BACTpipe: An assembly and annotation pipeline for bacterial genomics

Genomics_adventure ⭐ 17

Workshop on Genomics - Genomics Adventure

Java Genomics Toolkit ⭐ 16

Collection of scripts for working with Wiggle files and analyzing sequencing data

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Appliedgenomics2019 ⭐ 16

Materials for Spring 2019 Applied Genomics Course

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

a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly

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

Oyster_river_protocol ⭐ 10

Official Repository of the Oyster River Protocol for Transcriptome Assembly

Bioinformatics Toolbox ⭐ 10

Docker container for bioinformatics tools and pipelines

Polishclr ⭐ 10

A nextflow pipeline for polishing CLR assemblies

Banzai Microbialgenomics Pipeline ⭐ 10

Banzai is a Microbial Genomics Next Generation Sequencing (NGS) Pipeline Tool developed within Dr Scott Beatson’s Group at the University of Queensland

🌈Alignment-free scaffolding of genome assemblies with 10x Genomics Chromium reads

Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.

Fragment-Aware Local Assembly for Short-reads

Cg Pipeline ⭐ 6

Genome assembly/prediction/annotation pipeline for the Linux command line

Killigenomics ⭐ 6

Killifish genomics scripts

Appliedgenomeresearch ⭐ 6

course about NGS data processing: genomics and transcriptomics

Appliedgenomics2020 ⭐ 5

Description Materials for Spring 2020 Applied Genomics Course

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