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.