Metagenomics sequence formats
Please note, that most of our users problems are because the sequences are
- Not in Valid fasta format
- Not the right file formats
- Not nucleotide sequences. At the moment we don't have any service for annotating just protein sequences. If there is a large demand, we can add this, but you probably don't want to use genome annotation tools to annotate protein sequences anyway.
- See also Which Sequences Should I Upload, and Where
To upload sequence data to the metagenomics RAST server, we accept several file formats.
- You can upload a fasta file containing just the nucleotide sequences. This is the simplest format, just have a regular Valid fasta format nucleotide sequence file, and upload it. However, there may be some limitation on the file size.
- You can compress the sequence file containing just the nucleotide sequences with gzip, a popular compression tool. This will significantly reduce the size of the file to upload, and hence speed things up.
- You can also include a separate quality file in this same compressed file. To do this, compress both files into a single archive and then upload the archive.gz file (don't worry, we'll take care of the name, you can call it whatever you want!):
gzip archive.gz sequence.fa sequence.qual
If you do this, we will renumber the sequences and their corresponding quality scores at the same time. At the moment we don't use the quality scores, although we are experimenting with assembly tools that may take advantage of them. Therefore, the inclusion of quality scores is completely optional.