hello everebody please I am trying to assemble my reads using an algorithms for de novo assembly( De Bruijn Graph) and I don t know which algorith de novo more efficient in my case the optimal k using kmergenie is 17 Read Data : Ion Torrent, single end, percentage of GC 42, sequence length between 20 and 397
Thats a really poor dataset for de novo assembly as it contains only single end reads. Also, Ion torrent data contains lots of nasty indels which cause artificial frameshifts in predicted genes. Lastly, there is no long range information.
What coverage do you have ?
I would advise you to try soap2denovo and Spades. Potentially also Abyss.
By the way, shouldn't the genome be more like 600+ MBp ? https://www.nature.com/articles/ncomms3274