User: colindaven
colindaven • 790
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Posts by colindaven
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... Short reads can be best assembled on a single powerful machine. Eg. 1-2 TB RAM, 64 cores.
Long read assemblies are FAR FAR better. They need a cluster for best results, since a lot of CPU is needed for long read correction, overlapping and assembly. Or you could wait a long time (weeks) using a sin ...
written 13 days ago by
colindaven • 790
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... No. Unless you have long range information you're not going to get far. Otherwise a complete reassembly might be useful. Else the gold standard now is long reads, followed correction of the contigs by Illumina with Pilon / Racon ...
written 23 days ago by
colindaven • 790
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... The assembler CANU would appear to be a better option. ...
written 25 days ago by
colindaven • 790
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... Why not map your small contigs to a highly related reference genome to see what you would exclude ?
I would also do structural and functional annotation of contigs using eg prokka, interproscan or blast2go before excluding any short contigs. Why not look at the papers in GenomeAnnouncements or curr ...
written 25 days ago by
colindaven • 790
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... BLAST will be a lot more sensitive - allow more mismatches, and partial alignments - than BWA. ...
written 7 weeks ago by
colindaven • 790
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... Really difficult problem. It might make sense to search the raw reads for your insertion sequence - use python or grep.
In my experience neither de novo nor alignment strategies work well for this problem. A long read assembly would probably nail it, but noone seems to have the money for doing thos ...
written 7 weeks ago by
colindaven • 790
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... For what it's worth, here's my script which inserts subfeatures from (properly formatted) GFF3.
## Add tracks to JBrowse and print all subfeatures eg CDS and exons separately.
## You must be in the same directory
## Now supply the following GFF3 variable on the command line ...
written 7 weeks ago by
colindaven • 790
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... Do you mean that you want subfeature labels such as exons to be displayed ? I've never seen this done before. Are you sure the exon labels are also present in the database ? Using GFF3, I have seen labels such as ID, Name, Description and Note to be displayed slightly differently, experimentation is ...
written 7 weeks ago by
colindaven • 790
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... This is also an insightful piece from Heng Li:
http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use
...
written 7 weeks ago by
colindaven • 790
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... I would just assemble the new PacBio sequences de novo, eg with Canu. I would be surprised if you didn't have 40X + coverage.
The Pacbio assembly is going to be on a different planet to your existing assembly. The Illumina data can still be used to polish the assembly errors with Racon and or Pilon. ...
written 9 weeks ago by
colindaven • 790
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