1. Which one of these Velvet,SOAP And Abyss is best for a plant genome assembly?
2. correct or feasible to split the data for assembly and then merge/ combine the results of separate files at the end?
3. This will be the first assembly for my plant, according to my understanding I should go for a tool which provides better contigs at dis stage rather than scaffolds, your suggestion?
4. Which tool gives better scaffolds in case of plants?
What are the best tools for large genome de novo assembly i.e. of crop plants?
Dear Neelofar
All three software have strong algorithum for analysis however, abyss is user friendly and will take min. time to assemble the data but prerequisite for this the optimized kmer. for that we have to run it at different kmer values i.e. 21 to 99 (always odd no.) and have to find out best histogram at a particular kmer and finally we can run the software at selected kmer. For best kmer selection you can try kmergenie (http://bioinformatics.oxfordjournals.org/content/30/1/31.full.pdf+html).
Velvet is stronger than it but need more RAM to perform otherwise it will run into loophole.
First you generate good quality contigs than think about scaffolding that may become easier by using contigs.
All the best
Thank you so much sir for such a detailed answer. I hope I can come and discuss with you in case of any doubts.
Once you have your preliminary contigs you may consider using SSPACE for scaffolding (http://www.baseclear.com/bioinformatics-tools). Of course you will require mate-pair reads to do so.
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