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 93 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 genomics analysis pipelines
genomics genome variant-calling bam genome-sequencing illumina fastq genome-assembly variant-annotations viral-ngs viral
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Sep 20, 2024 - Python
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
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May 30, 2021 - Python
Long-reads Gap-free Chromosome-scale Assembler
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Mar 21, 2023 - Python
Learning to untangle genome assembly with graph neural networks.
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Nov 17, 2024 - Python
A program for assessing the T2T genome continuity
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Apr 9, 2025 - 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
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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Aug 8, 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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Sep 29, 2023 - Python
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
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Apr 11, 2025 - Python
C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.
genome assembly hi-c scaffolding hic genome-assembly phasing polyploid haplotype-assembly diploid genome-assembler haplotype-resolved-assembly hific pore-c ultra-long hifi-c
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Apr 13, 2025 - 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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Mar 5, 2025 - Python
An algorithm for centromere assembly using long error-prone reads
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May 25, 2021 - 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
Annotated Genome Optimization Using Transcriptome Information
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May 31, 2020 - Python
Reference genome quality scores
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Dec 17, 2020 - Python
⛓️ Construct a Physical Map from Linked Reads
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Apr 5, 2024 - Python
quality-control genome-annotation irma influenza genome-assembly sars-cov-2 rsv ncird-id cdc-influenza-division
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Mar 25, 2025 - Python
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