Genome Assembly tools are added by pipeline. Welcome contribute and get in touch!
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If there is an error in cited papers or tool does not included in list, please raise an ISSUE.
| Name | Introduction | Paper | Url | Note | Public Date |
|---|---|---|---|---|---|
| GenomeScope | Fast genome analysis from unassembled short reads. | Bioinformatics | Github | 2017.3 | |
| smudgeplot | Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc. | Nature Communications | Github | GenomeScope 2.0 | 2020.3 |
| Jellyfish | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. | Bioinformatics | Github | 2011.1 | |
| nQuire | A statistical framework for ploidy estimation using NGS short-read data. | BMC Bioinformatics | Github | 2018.4 | |
| KMC | Counting and manipulating k-mer statistics. | Bioinformatics | Github | 2017.5 | |
| KAT | a K-mer analysis toolkit to quality control NGS datasets and genome assemblies | Bioinformatics | Github | 2016.11 |
| Name | Introduction | Paper | Url | Note | Public Date |
|---|---|---|---|---|---|
| Hifiasm | Hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads. | Nat Methods | Github | 2021.2 | |
| HiCanu | designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). | Genome Research | Github | 2020.8 | |
| NextDenovo | NextDenovo is a string graph-based de novo assembler for long reads (CLR, |
bioRxiv | Github | 2023.3 | |
| IPA | Github | ||||
| Flye | De novo assembler for single molecule sequencing reads using repeat graphs. | Nature Methods | Github | 2020.10 | |
| Peregrine | Peregrine is a fast genome assembler for accurate long reads (length > 10kb, accuracy > 99%). | bioRxiv | Github | 2019.7 | |
| HGAP4 | HGAP4 is suitable for assembling a wide range of genome sizes and complexity. | Nature Methods | PacBio | 2013.5 | |
| Wtdbg2 | A fuzzy Bruijn graph approach to long noisy reads assembly. | Nature Methods | Github | 2019.12 | |
| Falcon | a set of tools for fast aligning long reads for consensus and assembly. | Nature Methods | Github | 2016.10 | |
| SMARTdenovo | Ultra-fast de novo assembler using long noisy reads. | Gigabyte | Github | 2021.3 | |
| miniasm | Ultrafast de novo assembly for long noisy reads (though having no consensus step) | Bioinformatics | Github | 2016.6 | |
| necat | Nanopore data assembler | Nature Communications | Github | 2021.1 | |
| Hypo-Assembler | A diploid genome polisher and assembler. | Nature Methods | Github | 2024.3 | |
| Verkko | a hybrid genome assembly pipeline developed for T2T assembly of HiFi or ONT reads. | Nature Biotechnology | Github | 2023.2 | |
| NextPolish2 | Repeat-aware polishing genomes assembled using HiFi long reads. | GPB | Github | 2024.1 | |
| Merfin | Evaluate variant calls and its combination with k-mer multiplicity. | Nature Methods | Github | 2022.3 | |
| SOAPdenovo2 | Next generation sequencing reads de novo assembler. | Bioinformatics | Github | 2015.1 | |
| Canu | A single molecule sequence assembler for genomes large and small. | Genome Research | Github | 2017.5 | |
| MECAT2 | Nature Methods | Github | 2017.9 | ||
| Name | Introduction | Paper | Url | Note | Public Date |
|---|---|---|---|---|---|
| 3D-DNA | Scaffold genome with Hi-C data. | Science | Github | Use Hi-C data | 2017.3 |
| LACHESIS | Use Hi-C data for ultra-long-range scaffolding of de novo genome assemblies. | Nature Biotechnology | Github | LACHESIS is no longer being actively developed. | 2013.12 |
| SALSA2 | A tool to scaffold long read assemblies with Hi-C data. | bioRxiv | Github | 2018.2 | |
| YaHS | Yet another Hi-C scaffolding tool. | Bioinformatics | Github | recommend | 2022.12 |
| instaGRAAL | Large genome reassembly based on Hi-C data, continuation of GRAAL. | Nature Communications | Github | NVIDIA graphics card is required | 2014.12 |
| EndHiC | a fast and easy-to-use Hi-C scaffolding tool. | Quantitative Biology | Github | 2021.11 | |
| Pin_hic | A Hi-C scaffolding method. | BMC Bioinformatics | Github | 2021.11 | |
| AutoHiC | A novel genome assembly pipeline based on deep learning. | bioRxiv | Github | recommend (Deep Learning) | 2023.8 |
| ALLHiC | phasing and scaffolding polyploid genomes based on Hi-C data. | Nature Plants | Github | recommend (Plant) | 2019.8 |
| Juicebox | a point-and-click interface for using Hi-C heatmaps to identify and correct errors in a genome assembly. | bioRxiv | Github | 2018.1 | |
| SLR | Scaffolding using long reads obtained by the third generation sequencing technologies. | BMC Bioinformatics | Github | 2019.10 | |
| LongStitch | Correct and scaffold assemblies using long reads. | BMC Bioinformatics | Github | 2021.10 | |
| RagTag | a collection of software tools for scaffolding and improving modern genome assemblies. | Genome Biology | Github | 2022.12 | |
| HapHiC | a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data. | bioRxiv | Github | 2023.11 | |
| scaffhic | Pipeline for genome scaffolding by modelling distributions of HiC pairs. | Github | |||
| HiCAssembler | Software to assemble contigs/scaffolds into chromosomes using Hi-C data. | Genes & Dev | Github | 2019.10 | |
| HaploHiC | comprehensive haplotype division of Hi-C PE-reads based on local contacts ratio. | Github | |||
| DipAsm | Efficient chromosome-scale haplotype-resolved assembly of human genomes. | bioRxiv | Github | 2020.7 |
| Name | Introduction | Paper | Url | Note | Public Date |
|---|---|---|---|---|---|
| YAGcloser | Yet-Another-Gap-Closer based on spanning of long reads. | Journal of Heredity | Github | 2022.5 | |
| TGS-Gapcloser | A gap-closing software tool that uses long reads to enhance genome assembly. | GigaScience | Github | 2020.9 | |
| DENTIST | Close assembly gaps using long-reads at high accuracy. | GigaScience | Github | 2022.1 | |
| Redundans | a pipeline that assists an assembly of heterozygous/polymorphic genomes. | Nucleic Acids Research | Github | 2016.4 | |
| Purge Haplotigs | an effective tool for the early stages of curating highly heterozygous genome assemblies produced from third-generation long read sequencing. | BMC Bioinformatics | Bitbucket | 2018.11 | |
| Purge_dups | haplotypic duplication identification tool. | Bioinformatics | Github | 2020.1 | |
| Pilon | an automated genome assembly improvement and variant detection tool. | PLOS ONE | Github | 2014.11 | |
| Racon | Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. | Genome Research | Github | 2017.1 | |
| nextpolish | Fast and accurately polish the genome generated by long reads. | Bioinformatics | Github | 2020.4 | |
| HaploMerger2 | Genome Research | Github | 2012.5 | ||
| GapFiller | Horticulture Research | Github | 2023.10 | ||
| RegCloser | BMC Bioinformatics | Github | 2023.6 |
Genome assembly evaluation tools.
| Name | Introduction | Paper | Url | Note | Public Date |
|---|---|---|---|---|---|
| QUAST | a quality assessment tool for evaluating and comparing genome assemblies. | Bioinformatics | Github | 2013.2 | |
| BioNanoAnalyst | a visualisation tool to assess genome assembly quality using BioNano data. | BMC Bioinformatics | Github | Use BioNano data | 2017.6 |
| CRAQ | Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement. | Nature Communications | Github | Single base scale | 2023.10 |
| BUSCO | assessing genome assembly and annotation completeness with single-copy orthologs. | Bioinformatics | BUSCO | 2015.6 | |
| Merqury | k-mer based assembly evaluation | Genome Biology | Github | 2020.9 | |
| Klumpy | A Tool to Evaluate the Integrity of Long-Read Genome Assemblies and Illusive Sequence Motifs. | bioRxiv | Bitbucket | ||
| GAEP | a comprehensive genome assembly evaluating pipeline. | JGG | Github | 2023.5 | |
| Flagger | Evaluating genome assemblies. | Nature | Github | 2023.5 | |
| Asset | assembly evaluation tool. | Github | |||
| Inspector | A tool for evaluating long-read de novo assembly results. | Genome Biology | Github | 2021.11 |