Remove vector sequences from genome database
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5 weeks ago
Helena ▴ 10

Hi,

I'm building a database containing Refseq genome sequences from selected bacterial species, which will be used for Nanopore sequencing of environmental samples.

In order to eliminate chances of false positives, I used the UniVec database to locate any potential contamination and got substantial hits to several vectors. I am pretty new to bioinformatics and therefore I wanted to hear if anyone has any ideas of how to mask/remove the contamination from the genome sequences?

/Helena

refseq univec vector database contamination • 194 views
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Are you only creating a database of main chromosomes from bacterial species? Normally the genomes may also include plasmids.

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To start I'll create a database containing the chromosomes and afterwards I'll create one for plasmids :) I have already separated the plasmid sequences from the chromosomes.

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5 weeks ago
colindaven ★ 3.3k

I also work on this, but for lung metagenomes chiefly. We have supplied ref seqs (unknown how useful for your purposes, as no plasmids) here: https://github.com/MHH-RCUG/Wochenende#installation

I wrote a contamination masking tool here, because otherwise it becomes a big source of false positives.

https://github.com/colindaven/blacklister

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