I am trying to carry out de novo assembly of a genome of interest. I have some queries regarding operation of velvet tool. When the k mers are selected and hash table is made, does velvet know which kmer is coming from which read?
" the hash table records the ID of the first read encountered containing that k-mer and the position of its occurrence within that read"-what does this exactly mean? A pictorial representation would be helpful.
"Each k-mer is recorded simultaneously to its reverse complement."- is it for paired end reads or in general? How does paired end read used in de brujin graph construction?
What does a twin node indicate? Is it for same k mer constructed from forward read or from the reverse read?
I have read zerbino's paper but still am a little confused on this matter.
Dear Diptarka Dasgupta,
Let me suggest to you 2 de novo assemblers which perform very well and are easy to use:
A5-pipeline: http://sourceforge.net/projects/ngopt/
and spades: http://bioinf.spbau.ru/spades
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools