Sequence Subsetting - Pgenerosa_v70 Genome Assembly with faidx

2019
Miscellaneous
Author

Sam White

Published

February 11, 2019

Steven asked to subset geoduck assembly in to >10kbp and >30kbp groups. Here are the commands, using faidx:

>10kbp subsetting

faidx --size-range 10000,1000000000 Pgenerosa_v070.fa > Pgenerosa_v071.fasta

Index new FastA

faidx Pgenerosa_v071.fasta

>30kbp subsetting

faidx --size-range 30000,1000000000 Pgenerosa_v070.fa > Pgenerosa_v073.fasta

Index new FastA

faidx Pgenerosa_v073.fasta

MD5 checksums

35b6b653b543ebb7f3631e68523ab595 Pgenerosa_v071.fasta ce81a0fc127e6cc0cbf216eb85b87749 Pgenerosa_v073.fasta

All files were copied to our genomic databank on Owl.

See our Genomic Resources wiki (GitHub) for a more concise overview.