assembly

此列表收集了与组装相关的工具，包括短读长、长度长和混合组装。

[SOAPdenovo2] - [C, r242, 2020.10] - [2012.12, GigaSci] - [SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.]
[idba/IDBA-UD] - [C++, v1.1.3, 2016.07] - [2012.04, Bioinformatics] - [IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth]
[SPAdes/metaSPAdes] - [C++, v4.0.0, 2024.06] - [2017.05, Genome Res] - [metaSPAdes: a new versatile metagenomic assembler.]
[megahit] - [C++, v0.3.3-a, 2015.7] - [2015.01, Bioinformatics] - [MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.]
[megahit] - [C++, v1.2.9, 2019.10] - [2016.6, Methods] -[MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices.]
[PenuiN] - [C, v5-cf8933, 2024.03] - [2024.08, bioRxiv] - [Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs.]
[BBMerge] - [Bash, v39.10, 2024.9] - [2017.10, PLoS One] - [BBMerge - Accurate paired shotgun read merging via overlap.]
[FLASH] - [C, v1.2.11, 2018.3] - [2011.9, Bioinformatics] - FLASH: fast length adjustment of short reads to improve genome assemblies.
[ABySS] - [C++/C, v2.3.9, 2024.9] - [2017.2, Genome Res] - [ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.]

[MaSuRCA] - [M4/Perl, v4.1.1, 2024.2] - [2013.8, Bioinformatics] - [The MaSuRCA genome assembler.]
[metaFlye] - [C/C++, v2.9.5, 2024.08] - [2020.10, Nat Methods] - [metaFlye: scalable long-read metagenome assembly using repeat graphs.]
[Canu] - [C++/C, v2.2, 2021.08] - [v2.3, 2024.12] - [2017.03, Genome Res] - [Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.]
[FALCON] - [Python, v0.3.0, 2018.08]
[miniasm] - [TeX/C, v0.3, 2018.07] - [2016.03, Bioinformatics] - [Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences.]
[wtdbg2] - [C, v2.5, 2019.09] - [2019.12, Nat Methods] - [Fast and accurate long-read assembly with wtdbg2.]
[Trycycler] - [Python, v0.5.5, 2024.03] - [2021.09, Genome Biol] - [Trycycler: consensus long-read assemblies for bacterial genomes.]
[NextDenovo] - [C, 2.5.2, 2023.03] - [2024.04, Genome Biol] - [NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads.]
[Autocycler] - [Rust, v0.1.2, 2024.12] - [A tool for generating consensus long-read assemblies for bacterial genomes]

[idba/IDBA-Hybrid] - [C++, v1.1.3, 2016.07] - [2012.04, Bioinformatics] - [IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth]
[SPAdes/metaSPAdes] - [C++, v4.0.0, 2024.06] - [2017.05, Genome Res] - [metaSPAdes: a new versatile metagenomic assembler.]
[Aviary] - [Python, v0.9.2, 2024.09] - [A hybrid assembly and MAG recovery pipeline (and more!)]
[OPERA-MS] - [C++/Python, v0.8.3, 2020.06] - [2019.07, Nat Biotechnol] - [Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes.]
[Unicycler] - [C++, v0.5.1, 2024.07] - [2017.06, PloS Comput Biol] - [Unicycler: resolving bacterial genome assemblies from short and long sequencing reads.]
[MaSuRCA] - [M4/Perl, v4.1.1, 2024.2] - [2017.5, Genome Res] - [Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm.]
[HyLight] - [C++/Python, v1.0.0, 2024.9] - [2024.10, Nat Commun] - [HyLight: Strain aware assembly of low coverage metagenomes.]

PB HiFi

[hifiasm-meta] - [C++, v0.3.2, 2024.9] - [2024.04 Genome Biol] - [Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies.]
[metaMDBG] - [C++, v1.0, 2024.8] - [2024.1, Nat Biotechnol] - [High-quality metagenome assembly from long accurate reads with metaMDBG.]

[FMLRC2] - [Rust, v0.1.8, 2022.07] - [2023.03, Mol Bio Evo] - [Polishing de novo nanopore assemblies of bacteria and eukaryotes with FMLRC2.]
[pilon] - [Scala, v1.24, 2021.01] - [2014.11, Plos ONE] - [Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement.]
[NextPolish] - [Rust, v1.4.1, 2022.07] - [2019.11, Bioinformatics] - [NextPolish: a fast and efficient genome polishing tool for long read assembly.]
[Polypolish] - [Rust, v0.6.0, 2024.01] - [2024.06, Microbial Genomics] - [How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies.]
[Pypolca] - [Python, v0.3.1, 2024.02] - [2024.06, Microbial Genomics] - [How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies.]
[MaSuRCA/POLCA] - [M4/Perl, v4.1.1, 2024.2] - [2020.6, PLoS Comput Biol] - [The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies.]
[Racon] - [C++, v1.5.0, 2021.12] - [2017.1, Genome Res] - Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.

LRGE - [Rust, 2024.12, v0.1.3] - [2024.12, bioRxiv] - Genome size estimation from long read overlaps.