Miseq v2 PE library length for Allpaths-LG
Hello,
I'd like to use ALLPATHS-LG for de novo assembling of a fungal genome
(~20 Mbp). I will use Miseq data for the assembling.
I am wondering the length of fragment for paired read can be longer for the version2 of Miseq.
In the FAQ of Allpaths-LG, there is a sentence "For longer reads, somewhat longer fragments could be used".
###################################
Q: Do I need paired reads from an “overlapping” fragment library?
Yes. We use paired reads of length ~100 bases from fragments of size ~180 bp. For longer reads, somewhat longer fragments could be used.
###################################
Now the read length of the Miseq v2 is 250 bp, paired reads from fragments of more than size ~400 bp would be overlapping and can be input for ALLPATHS-LG, right?
Has anyone try to input overlapping fragment library from the fragments of
more than 400 bp?
Many thanks,
I'd like to use ALLPATHS-LG for de novo assembling of a fungal genome
(~20 Mbp). I will use Miseq data for the assembling.
I am wondering the length of fragment for paired read can be longer for the version2 of Miseq.
In the FAQ of Allpaths-LG, there is a sentence "For longer reads, somewhat longer fragments could be used".
###################################
Q: Do I need paired reads from an “overlapping” fragment library?
Yes. We use paired reads of length ~100 bases from fragments of size ~180 bp. For longer reads, somewhat longer fragments could be used.
###################################
Now the read length of the Miseq v2 is 250 bp, paired reads from fragments of more than size ~400 bp would be overlapping and can be input for ALLPATHS-LG, right?
Has anyone try to input overlapping fragment library from the fragments of
more than 400 bp?
Many thanks,