I am trying to import a folder which contains multifasta files. These multifasta files are demultiplexed into their respective barcodes and selected for size in terms of the length of the DNA sequence.
Origin of raw sequences:
The raw sequences were obtained from MInION sequencer by Nanopore technologies, basecalled and demultiplexed using albacore. The resulting demultiplexed multifastq sequences were converted to fasta format and then selected for a particular size range.
I have tried qiime tool import using FeatureData[Sequence] since the file is in FASTA format. However this only supports importing one multifasta file at a time instead of the entire folder.
What I am trying to do is to add the qiime labels as done in qiime1 to these multifasta fasta which will produce a single combined multifasta file with the labels added. I assume the option for this would be to merge the combined multifasta file with the mapping-_file. Am I right?
We don’t have a format that supports this representation of the data. My recommendation is to go back to your demultiplexed fastq and import that - then you will have more options available to you. If you are insistent on working with fasta records, you could get these data in the QIIME 1 post_split_libraries.py format, then import that. Let us know how it goes!
(Matthew Ryan Dillon)
Thank you very much. I figured those would be my two options and I am working on them right now.
However is there a possibility that the option of using fasta records as a folder containing the multifasta files will be implemented in qiime2 in the future?
Another question that I also have is that for how long will the qiime1 platform remain available given that everyone is transitioning to qiime2. As this would be a problem if I would need to use the add_qimme_labels.py format from qiime1 then import to qiime2.
For sure! One of my favorite parts of QIIME 2 is that it is modular - anyone is free to make a new plugin defining new methods, types, and formats! As well, the QIIME 2 plugins that we develop as part of the "core" distribution are all open source - we welcome contributions!