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Forum: Pacific Biosciences 12-08-2016, 08:48 AM
Replies: 3
Views: 2,707
Posted By nwfungi
Question trouble shooting PB assembly generating a larger than expected contig

So I've got a newly assembled genome that was sequenced using PacBio sequencing and obtained >100x coverage. It was assembled with HGAP.3 and for the most part looks great except for an exceptionally...
Forum: Pacific Biosciences 03-01-2016, 04:53 AM
Replies: 6
Views: 2,407
Posted By nwfungi
Help: de novo assembly using SMRT portal and hgap.3

Problem: Extremely new to assembly and attempting to execute de novo assembly using hgap.3 in SMRT portal using 9 SMRTcells. lambda example data provided runs fine so I assume that there isn't a...
Forum: Bioinformatics 12-04-2015, 07:05 AM
Replies: 7
Views: 3,702
Posted By nwfungi
Thanks for all the information and apologies for...

Thanks for all the information and apologies for slow response time.

As for the PB data I have, it is in fastq format and we are in the process of trying to get the original files but this...
Forum: Bioinformatics 12-02-2015, 12:19 PM
Replies: 7
Views: 3,702
Posted By nwfungi
Fungal Genome Assembly... a painful experience

Hi all and thanks for any insight you have in advance.

I am trying to assemble a fungal genome of approximately 42Mb in size. I have reads from an Ion Torrent run and some old data our lab had...
Forum: Bioinformatics 11-17-2015, 02:28 PM
Replies: 4
Views: 2,048
Posted By nwfungi
Talking Pulling together contigs: a less stringent assembly


New grad student here working with a fungi with a genome that is roughly 42-50Mbs. Basically what I'm trying to do is an assembly with filtered sub reads in fastq format which came from...
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