genome-assembly
There are 262 repositories under genome-assembly topic.
ablab/spades
SPAdes Genome Assembler
voutcn/megahit
Ultra-fast and memory-efficient (meta-)genome assembler
jts/nanopolish
Signal-level algorithms for MinION data
malonge/RagTag
Tools for fast and flexible genome assembly scaffolding and improvement
Nextomics/NextDenovo
Fast and accurate de novo assembler for long reads
broadinstitute/viral-ngs
Viral genomics analysis pipelines
DRL/blobtools
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
oushujun/LTR_retriever
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.
malonge/RaGOO
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
TheGeekiestOne/Coursera-Data-Structures-and-Algorithms-Specialization
Master Algorithmic Programming Techniques. Learn algorithms through programming and advance your software engineering or data science career
Gabaldonlab/redundans
Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
linzhi2013/MitoZ
MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
mcveanlab/mccortex
De novo genome assembly and multisample variant calling
neherlab/pangraph
A bioinformatic toolkit to align genome assemblies into pangenome graphs
vpc-ccg/haslr
A fast tool for hybrid genome assembly of long and short reads
lvrcek/GNNome-assembly
Learning to untangle genome assembly with graph neural networks.
algbio/ggcat
Compacted and colored de Bruijn graph construction and querying
kishwarshafin/helen
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
ganlab/GALA
Long-reads Gap-free Chromosome-scale Assembler
HuffordLab/NAM-genomes
Detailed bioinformatics scripts and methods used in the NAM genome paper.
HingeAssembler/HINGE
Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"
BioJulia/GenomeGraphs.jl
A modern genomics framework for julia
tanghaibao/allhic
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
bcgsc/tigmint
⛓ Correct misassemblies using linked AND long reads
nf-core/bacass
Simple bacterial assembly and annotation pipeline
JiaoLaboratory/CRAQ
Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement
fmalmeida/MpGAP
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
Nextomics/NextPolish2
Repeat-aware polishing genomes assembled using HiFi long reads
a-ludi/dentist
Close assembly gaps using long-reads at high accuracy.
linxingchen/cobra
A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.
brentp/indelope
find large indels (in the blind spot between GATK/freebayes and SV callers)
BeatsonLab-MicrobialGenomics/micropipe
A pipeline for high-quality bacterial genome construction using ONT sequencing
koszullab/instaGRAAL
Large genome reassembly based on Hi-C data, continuation of GRAAL
CMU-SAFARI/BLEND
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)
Adamtaranto/teloclip
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
yeeus/GCI
A program for assessing the T2T genome continuity