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Top 14 genome-assembly open source projects

De novo genome assembly and multisample variant calling

✭ 105

c Makefile perl python r shell genomics variant-calling kmer cortex genome-analysis genome-assembly de-bruijn-graphs genome-graph contigs

CAMSA

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

✭ 18

python javascript HTML powershell CSS Batchfile shell genomics comparative-genomics genome-assembly genome-scaffolding scaffold-assembly asssembly-reconciliation

fast-sg

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

✭ 22

C++perl shell Makefile awk nanopore pacbio scaffolding illumina genome-assembly hybrid-genome-assembly alignment-free-algorithm

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.

✭ 131

perl Dockerfile genome-annotation genome-assembly ltr-retrotransposons lai ltr-retriever

dentist

Close assembly gaps using long-reads at high accuracy.

✭ 39

d shell python docker bioinformatics snakemake cluster singularity dub pacbio genome-assembly daligner long-reads gap-filling close-assembly-gaps damapper

indelope

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

✭ 38

nim c shell genomics vcf variant-calling k-mer-counting genome-assembly nim-lang local-assembly

redundans

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

✭ 90

perl python shell bioinformatics pipeline genomics docker-image polymorphic closing fasta scaffolding assembled-contigs genome-assembly paired-end contigs heterozygous mate-pairs

haslr

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

✭ 68

C++python c Makefile bioinformatics nanopore genomics pacbio genome-assembly long-reads hybrid-assembly

instaGRAAL

Large genome reassembly based on Hi-C data, continuation of GRAAL

✭ 32

Cuda python genomics hi-c scaffolding 3c genome-assembly

HINGE

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

✭ 63

C++python c Jupyter Notebook Nix shell genome-assembly

LRSDAY

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

✭ 26

perl shell Makefile c Visual Basic 6.0 python genomics genome-annotation oxford-nanopore genome-assembly yeast pacbio-data yeastgenome

downpore

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

✭ 32

go assembly long-read genome-assembly genome-scaffolding genome-mapping

MGSE

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

✭ 22

python genomics genome ngs plants pacbio illumina genome-assembly read-mapping ont nanopore-sequencing genome-size-estimation

berokka

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

✭ 23

perl Makefile bioinformatics genomics genome-assembly long-read-sequencing circular-genome

1-14 of 14 genome-assembly projects