NCBI Contamination Screen

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4.5 years ago

Pegasus ▴ 120

Hi all,

I have medusa-scaffold data, which contain 160 scaffolds and some NNN bridges. The file is in fasta format, I need to remove all scaffolds less than 200, and vectors possible contamination, this why I am trying to use NCBI Vecscreen. VecScreen However, as a beginner, I still do not know where can I find the option of removing these <200 bp, and how to upload my fasta data, since I have no accession number yet.

Please let me know if you are familiar with such a tool. Many thanks!

next-gen genome • 1.1k views

ADD COMMENT • link 4.5 years ago by Pegasus ▴ 120

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If you are looking to simply remove sequences that are <200 bp (no screening per se) then you can use BBtools.

reformat.sh in=your.fa out=filtered.fa minlength=200

ADD REPLY • link 4.5 years ago by GenoMax 148k

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Thanks genomax can this code be used in the mac terminal!

ADD REPLY • link 4.5 years ago by Pegasus ▴ 120

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Yes. BBTools are written in java. So you just need Java runtime.

ADD REPLY • link 4.5 years ago by GenoMax 148k

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Hi, biomax, please check the edited question. Thanks in advance for your valuable answers