Tools for fast and flexible genome assembly scaffolding and improvement
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Feb 14, 2024 - Python
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genome-assembly
Here are 120 public repositories matching this topic...
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
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Aug 21, 2024 - Python
viral-ngs: command line tools and wrappers for processing raw viral genomic data
python docker bioinformatics genomics genome ngs variant-calling bam genome-sequencing illumina fastq genome-assembly variant-annotations viral-ngs viral
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Apr 27, 2026 - Python
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
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May 30, 2021 - Python
A program for assessing the T2T genome continuity and completeness
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Feb 28, 2026 - Python
C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on 3C-based data (Pore-C, CiFi, Hi-C，Omni-C).
genome assembly hi-c scaffolding hic genome-assembly phasing polyploid haplotype-assembly diploid genome-assembler haplotype-resolved-assembly pore-c ultra-long cifi omni-c
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Jan 25, 2026 - Python
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.
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Sep 8, 2025 - Python
Long-reads Gap-free Chromosome-scale Assembler
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Mar 21, 2023 - Python
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
genomics genome-sequencing genomes oxford-nanopore genome-analysis genome-assembly genomic-data-analysis genome-scale-models human-genetics
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Oct 28, 2020 - Python
Learning to untangle genome assembly with graph neural networks.
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Nov 17, 2024 - Python
A novel genome assembly pipeline based on deep learning
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Dec 2, 2024 - Python
⛓ Correct misassemblies using linked AND long reads
bioinformatics genome-assembly genome-scaffolding 10xgenomics misassembly-correction linked-reads bioinformatics-tool
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Mar 24, 2026 - Python
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
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Apr 21, 2026 - Python
Visualization tool for (meta)genome assembly graphs
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Apr 29, 2026 - Python
Large genome reassembly based on Hi-C data, continuation of GRAAL
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Apr 27, 2026 - Python
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
genomics genome ngs plants pacbio illumina genome-assembly read-mapping ont nanopore-sequencing genome-size-estimation
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Jul 11, 2025 - Python
A snakemake workflow for de novo genome assembly. It produces chromosome-scale primary/phased assemblies complete with organelles (mitochondrion and/or chloroplast). It automatically assesses the quality of the results.
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Apr 7, 2026 - Python
CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies
python genomics comparative-genomics genome-assembly genome-scaffolding scaffold-assembly asssembly-reconciliation
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Apr 13, 2020 - Python
An algorithm for centromere assembly using long error-prone reads
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May 25, 2021 - Python
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