Dump fastq to sra-lite

[ledwmp]

Is there documentation on which flags to use to dump fastq to sra-lite format?

We are trying to standardize some of our pipelines, and have some data in sra-lite format and others as fastq. It seems using latf-load followed by kar is probably the right path, but it's unclear how to run a conversion from fastq to sra-lite.

Thanks, any help would be appreciated.

[durbrow]

You are correct. The generation of the sra-lite files happens inside the SRA ingest pipeline at NCBI. That pipeline uses the toolkit but it isn't a part of the toolkit and the toolkit team is not qualified to describe the intricacies of the process (IOW it is complicated and I don't know all of the steps involved.)

We may be able to modify latf-load to produce the sra-lite output directly. If you were to request it and aren't interested in the full quality version... (It is mostly the removal of the quality column after ensuring that we record that the it indicated low quality.)

Please let us know. We are interested in helping you with this.

[ledwmp]

Adding that functionality to latf-load would be great.

It's a little unclear in the documentation when the vendor flag is used to set the pass|filter flag, when quality scores are used to set the flag, and how these filters work. Otherwise, we would probably attempt to implement these filters ourselves.

Adding this functionality to latf-load would ensure consistency with the sra-lite format. We appreciate your help!