inchworm and paired ends

[ians]

I recently read in the installation README that:

"There is no 'paired read' mode currently in inchworm. It treats each read independently. If you have pairs, just include them all in a single fasta file with the sequences properly oriented for strand-specificity (sense strand)."

Does this mean that inchworm does not take insert size information inconsideration when assembling scaffolds?

Does Butterfly use insert size info to assemble scaffolds?

[usad]

If it said so in the read-me....

However Butterfly should use read pairs. You might want to download the whole Trinity package and read the manuscript

http://www.nature.com/nbt/journal/v29/n7/full/nbt.1883.html

[cedance]

ians, imo 'no paired read' mode means the same you infer to me as well = no insert size info.

[upendra_35]

Hi ians,

I think Trinity do accept Paired End Reads as separate files. Please refer to Trinity Manual for more information.

http://trinityrnaseq.sourceforge.net/

[ians]

Thanks for all the feedback!