how to remove pig sequences from metagenomics data

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5.8 years ago

g.feng • 0

hello, I am working on metagenomics data from pig faecal samples. I want to remove pig sequences from the samples using bowtie2 before running humann2. However, I could not find a pig genome database, like the hg19 for human. Do anyone have any idea how can I remove the pig sequences? Thank you.

next-gen • 1.5k views

ADD COMMENT • link updated 5.6 years ago by Biostar 20 • written 5.8 years ago by g.feng • 0

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Go to the UCSC genome browser page and search for susScr11 or pig

ADD REPLY • link 5.8 years ago by Arup Ghosh 3.2k

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Like Pig Reference Genome?

ADD REPLY • link 5.8 years ago by ATpoint 85k

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I could not find a pig genome database

seriously? here's a second one just three keystrokes away from the NCBI landing page

Sus scrofa at the NCBI leads you to 16 assemblies...

ADD REPLY • link 5.8 years ago by Carambakaracho ★ 3.3k

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on google pig genome download + ncbi + hit enter HARD

ADD REPLY • link 5.6 years ago by lakhujanivijay 5.9k

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