De novo
TODO:
Tools
| Name | Main feature |
|---|---|
| ABySS2 | An assembler intended for SGS PE and linked reads. |
| AllPath-LG | Uses a unipath graph from the k-mer paths to collapse repeats. |
| MEGAHIT | An ultrafast and memory-efficient assembler for SGS reads. |
| SOAPdenovo | De Bruijn graph assembler with an error correction stage. |
| Falcon/HGAP | Diploid-aware mode including trim, correction, and consensus for PacBio reads. |
| CANU | A fork of the Celera Assembler, including trim, correction, and consensus for TGS reads. |
| SMARTdenovo | De novo assembler including all-vs.-all raw read alignments without an error correction stage for TGS reads. |
| MECAT | Ultrafast mapping, error correction, and de novo assembly tools for single-molecule sequencing reads. |
| Flye | A repeat graph mode including trim, correction, and consensus with polishing for TGS reads. |
| Shasta | A run-length representation of ONT reads. |
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