Convert from Qiime2 database (2 files) to vsearch database (1 fasta file)

General Discussion
1

Hello everyone,

I am a beginner using Qiime2 for metabarcoding data analyses, and I am encounter a difficulty with the taxonomic assignment. I saw another discussion post about converting vsearch format database into Qiime2 database for taxonomic assignment. Link here: (Converting a USEARCH UNITE ITS database to QIIME 2 format)

However, I was trying to do exactly the opposite, which is to convert from the Qiime2 database (2 files, one taxa file and one fasta file) to a database that is compatible with vsearch or other programs (1 file, could be a fasta file where the header contains all the information in formats such as sintax, and the following row is the sequence). I was wondering if there are any options?

For example, the first 5 rows in the taxa file are
U02002 k__Metazoa;p__Arthropoda;c__Malacostraca;o__Decapoda;f__Alpheidae;g__Alpheus;s__Alpheus_canalis U02003 k__Metazoa;p__Arthropoda;c__Malacostraca;o__Decapoda;f__Alpheidae;g__Alpheus;s__Alpheus_canalis U02004 k__Metazoa;p__Arthropoda;c__Malacostraca;o__Decapoda;f__Alpheidae;g__Alpheus;s__Alpheus_cristulifrons U02005 k__Metazoa;p__Arthropoda;c__Malacostraca;o__Decapoda;f__Alpheidae;g__Alpheus;s__Alpheus_cristulifrons U02006 k__Metazoa;p__Arthropoda;c__Malacostraca;o__Decapoda;f__Alpheidae;g__Alpheus;s__Alpheus_cristulifrons

The first 5 rows in the sequence file are (there is a > at the beginning of each line but missing here on the website due to formatting):

U02002
CCAATCCTTTACCAACATCTATTCTGATTCTTCGGACACCCAGAAGTTTACATTTTAATTCTCCCAGCTTTCGGTATAATCTCCCATATTATTAATCAAGAATCAGGGAAAAAAGAAGCATTCGGAACACTAGGTATAATCTATGCAATAGCAGCAATTGGAATCCTTGGGTTTGTAGTATGAGCACACCACATATTCACTGTTGGTATAGACGTAGACACACGAGCCTACTTCACATCAGCAACTATAATTATTGCAGTTCCCACAGGAATTAAAATTTTCAGGTGACTAGGAACCCTACACGGAAGACAATTCACCTACAGACCATCACTACTTTGAGCCCTAGGATTCGTATTCCTATTCACAATAGGAGGACTAACCGGTGTAGTACTAGCGAACTCATCTATTGACATTATCCTTCACGACACTTATTATGTAGTAGCACATTTCCACTACGTACTGTCCATAGGAGCTGTATTTGGAATCTTTGCAGGTATTGCTCATTGATTCCCCCTATTCACAGGACTATCACTAAACCCACAATGACTAAAAATACACTTTTTCACTATATTCATTGGAGTAAATATTACATTCTTCCCTCAACACTTCCTTGGATTAAACGGTATGCCA
U02003
TTTTGATTCNTCGGTCACCCCGAAGTCTACATTCTTATTCTACCAGCTTTCGGTATAATCTCCCATATTATTAACCAAGAATCAGGGAAAAAGGAAGCGTTCGGGACACTAGGTATAATCTACGCAATAGCAGCAATTGGAATCCTTGGATTTGTAGTATGGGCACATCACATGTTCACAGTTGGTATAGATGTAGACACACGAGCCTACTTTACATCAGCAACTATAATTATTGCAGTTCCCACTGGAATTAAAATTTTCAGGTGGCTAGGAACCCTGCACGGGAGACAATTCACCTACAGACCATCACTACTTTGAGCCCTAGGGTTCGTATTCCTATTCACAATAGGTGGACTAACCGGTGTGGTACTAGCAAACTCATCTATAGATATTATCCTCCACGACACTTATTATGTAGTAGCACACTTCCACTATGTCCTGTCAATAGGAGCCGTATTCGGGATCTTTGCAGGTATTGCTCATTGATTCCCCCTATTCACAGGGTTATCTCTAAACCCCCAGTGACTTAAAATGCACTTTTTCACTATATTCATTGGAGTAAACATTACATTCTTCCCACAACACTTCCTTGGGCTAAACGGAATGCCTCGACGGTACTCTGACTACCCAGACGCTTATACT
U02004
ATTCTATATCAACATCTATTCTGATTCTTTGGGCACCCTGAAGTGTATATTTTAATCCTACCCGCTTTTGGAATAATCTCCCACATTATCAACCAAGAATCCGGTAAAAAAGAAGCATTTGGAACACTAGGTATGATCTACGCCATAGCAGCCATTGGTATCCTTGGTTTCGTAGTGTGGGCCCATCATATATTTACAGTAGGCATGGACGTTGACACTCGAGCCTACTTTACATCTGCAACTATAATTATTGCAGTTCCCACTGGAATTAAAATTTTCAGATGATTAGGAACATTACATGGAAGTCAGTTCACTTACAGACCATCCCTACTCTGAGCCCTGGGATTTGTATTCCTATTCACTATAGGAGGTCTCACGGGAGTAGTCCTAGCTAACTCTTCCATCGATATCATCCTTCACGACACCTATTATGTTGTAGCCCATTTCCACTACGTCCTATCAATAGGAGCCGTCTTTGGAATCTTTGCAGGAATCGCCCACTGATTCCCACTATTTACCGGTCTATCTCTGAATCCTCAATGACTTAAAATACACTTCTTTACTATATTTATCGGAGTTAATATCACATTCTTCCCACAACACTTCTTAGGCCTGAATGGAATACCTCGACGATAC
U02005
CTTTACCAACACCTATTNNNNNNNNTNNNTCACCCAGAGGTTTACATTTTAATTCTACCGCCTCTTGGTATAATNTCCCACATTATAAATCAAGAGTNCGGCAAAAAAGAAGCNTTCGGAACATTAGGTATAATTTACGCAATAGCAGCAATCGGTATCCTAGGCTTNGTAGTATCAGCCCATCATATGTTTACTGTTNNNNNNNNNNNNGACACACGAGCCTATTTCACCTCAGCAACTATAATTATTGCAGTCCCTACAGGAATTAAAATCTTCAGATGACTGAGAACTCTACATGGTACACAATTCACATATAGACCCTCTCTTTTATGGGCCTTAGGATTTGTATTCCTATTCACTATAGGAGGTTTAACAGGAGTAATTTTAGCTAACTCCTCTATTGATATNATCTTACATGACACTAACTNTGTTGTAGCACACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGGAANNTTCGCCGGAATCGCCCATTGATTCCCCCTCTTTACAGGACTATCATTAAACCCAAAATTACTTAAAATACNCTTCTTTACTATATTNNNCGGAGTTAACATTACATTCTTCCCCCAACACTTCTTGGGG
U02006
CACCCAGAGGTTTACATTTTAATTCTACCAGCCTTTGGTATAATCTCCCACATTATAAATCAAGAGTCCGGCAAAAAAGAAGCATTCGGAACATTAGGTATAATTTACGCAATAGCAGCAATCGGTATCCTAGGCTTTGTAGTATGAGCCCATCATATGTTTACTGTTNNNNNNNNNNNNGACACACGAGCCTATTTCACCTCAGCAACTATAATTATTGCAGTACCTACAGGAATTAAAATCTTCAGATGACTGAGAACTCTACATGGTACACAATTCACATATAGACCCTCTCTTTTATGGGCCTTAGGATTCGTGTTCCTATTTACTATAGGAGGTTTAACAGGAGTAATTTTAGCTAACTCCTCTATTGATATTATCTTACACGACACCTATTATGTTGTAGCACACTTCCAATATGTCCTATCAATAGGAGCTGTATTTGGAATTTTCGCGGGGATCGCCCATTGATTCCCACTCTTTACAGGGCTATCATTAAACCCTAAATGACTTAAAATACACTTCTTTACTATATTCATCGGGGTTAACATTACATTCTTCCCC

And below is something I want:

U02002;tax=d:Eukaryota;p:Arthropoda;c:Malacostraca;o:Decapoda;f:Alpheidae;g:Alpheus;s:Alpheus_canalis
CCAATCCTTTACCAACATCTATTCTGATTCTTCGGACACCCAGAAGTTTACATTTTAATTCTCCCAGCTTTCGGTATAATCTCCCATATTATTAATCAAGAATCAGGGAAAAAAGAAGCATTCGGAACACTAGGTATAATCTATGCAATAGCAGCAATTGGAATCCTTGGGTTTGTAGTATGAGCACACCACATATTCACTGTTGGTATAGACGTAGACACACGAGCCTACTTCACATCAGCAACTATAATTATTGCAGTTCCCACAGGAATTAAAATTTTCAGGTGACTAGGAACCCTACACGGAAGACAATTCACCTACAGACCATCACTACTTTGAGCCCTAGGATTCGTATTCCTATTCACAATAGGAGGACTAACCGGTGTAGTACTAGCGAACTCATCTATTGACATTATCCTTCACGACACTTATTATGTAGTAGCACATTTCCACTACGTACTGTCCATAGGAGCTGTATTTGGAATCTTTGCAGGTATTGCTCATTGATTCCCCCTATTCACAGGACTATCACTAAACCCACAATGACTAAAAATACACTTTTTCACTATATTCATTGGAGTAAATATTACATTCTTCCCTCAACACTTCCTTGGATTAAACGGTATGCCA

Thank you!

2

Hi @Tim_Z ,
No there is no way to do this transformation with QIIME 2, nor am I aware of an external program to do this easily. You could use R or Python to do this.

Good luck!

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3

As for the format after combining, it does not necessarily have to be sintax format and could be other commonly used formats as well. I am just trying to see if it's possible to convert it into one database file, where the first row contains species name/accession number and the second row is the sequence.

4

Hi @Tim_Z,

This would be something you'd have to do using a custom script that you'd create in R or Python, as @Nicholas_Bokulich suggested. There aren't any existing tools that we are aware of that provide this functionality. Best of luck :lizard:

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