| IBDA-UD |
A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. |
22495754 |
| MEGAHIT |
A fast and scalable metagenome assembler driven by advanced methodologies and community practices. |
27012178 |
| metaSPAdes |
SPAdes is a versatile toolkit designed for assembly and analysis of sequencing data. SPAdes is primarily developed for Illumina sequencing data, but can be used for IonTorrent as well. |
28298430 |
| MetaVelvet |
A de novo metagenome assembly from short sequence reads. |
22821567 |
| MetaVelvet-SL |
An extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning. |
25431440 |
| MetaVelvet-DL |
A MetaVelvet deep learning extension for de novo metagenome assembly. |
34078257 |
| metaplasmidSPAdes |
Plasmid detection and assembly in genomic and metagenomic data sets. |
31048319 |
| metaviralSPAdes |
A assembly of viruses from metagenomic data. |
32413137 |
| Vclust |
Ultrafast and accurate sequence alignment and clustering of viral genomes. |
bioRxiv |
| OPERA-MS |
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. |
31359005 |
| Canu |
A scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. |
28298431 |
| metaFlye |
A scalable long-read metagenome assembly using repeat graphs. |
33020656 |
| NECAT |
Efficient assembly of nanopore reads via highly accurate and intact error correction. |
33397900 |
| MECAT |
Fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. |
28945707 |
| wtdbg2 |
A de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). |
31819265 |
| Shasta |
A long read assembler. |
32686750 |
| metaMDBG |
High-quality metagenome assembly from long accurate reads. |
38168989 |
| SMAGLinker |
Integrate single amplified genome (SAG) and metagenome to reconstruct qualified microbial genomes. |
34641955 |
| ccSAG |
Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes. |
29391438 |