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27 search results found

Nanopolish ⭐ 496

Signal-level algorithms for MinION data

Megahit ⭐ 442

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

Redundans ⭐ 121

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

Mccortex ⭐ 86

De novo genome assembly and multisample variant calling

Pangraph ⭐ 72

A bioinformatic toolkit to align genome assemblies into pangenome graphs

Compacted and colored de Bruijn graph construction and querying

⛓ Correct misassemblies using linked AND long reads

Close assembly gaps using long-reads at high accuracy.

Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement

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

Nam Genomes ⭐ 34

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

Genomegraphs.jl ⭐ 29

A modern genomics framework for julia

Goldrush ⭐ 26

Linear-time de novo Long Read Assembler

Teloclip ⭐ 26

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

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)

Metagenomescope ⭐ 22

Visualization tool for (meta)genome assembly graphs

Score Assemblies ⭐ 20

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

⛓️ Construct a Physical Map from Linked Reads

Bioinformatics Tools ⭐ 14

Small and simple scripts useful for various bioinformatics purposes e.g. extract sequences from fasta files

Reference genome quality scores

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

Angelfish Genome Assembly ⭐ 12

This is a pipeline describing how I assembled the complete genome of the freshwater angelfish, Pterophylllum scalare.

Genomicscourse ⭐ 11

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

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

Modular Assembly Hs18 ⭐ 9

Mix and match modular genome assembler components

A pipeline to use Lep-Map3 to create linkage maps and LepAnchor for anchoring and orienting genome assemblies with said linkage maps.

guided genome assembler using colored overlap graphs

A minimal Python library for parsing SPAdes FASTG files

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