Best open source de novo assembler till date??

Question

[sangram_keshari]

I came across literally many open source de novo assembly tools having their own criteria. Some are very old, But having a strong citation. And some are very new promising to be better than those existing ones. So suggestions please.

[GenoMax]

Depends on what kind of data you have and the expected genome size.

"Best" is relative. Someone's best may not work for your data at all.

[sangram_keshari]

Okay if it is Transcriptome assembly? An i have paired reads?? Then

[GenoMax]

For eukaryotic genomes Trinity for RNAseq assembly. Consider the computing requirements for Trinity carefully first.

For smaller genomes rnaSPAdes may be useful.

[WouterDeCoster]

Does your tag of "rna-seq" indicate that you are looking for de novo transcriptome assembly? Because that's an important difference. Your question is highly dependent on the technology used, the ploidy, genome size, repeat content, read length and coverage.

[sangram_keshari]

Reads are from Illumina, Pared end reads and yes i was talking about transcriptome assembly. Then what transcriptome assemblyshould i go for?

[WouterDeCoster]

I'm not doing transcriptome assembly myself, but based on what I read Trinity is the most used (which doesn't necessarily make it the best). I saw a bit ago this paper and this looks definitely worth trying: SuperTranscript: a data driven reference for analysis and visualisation of transcriptomes