Commit fa345b44 authored by Mathieu Giraud's avatar Mathieu Giraud

doc/workflow.md: workflow and file formats, draft

parent 15dfb96b
# Post-sequencer workflow before upload to a Vidjil server
This help is intended for bioinformaticians preparing workflows after their sequencer output.
See also considerations on [libraries and recombinations](locus.md).
## File formats
It is recommended to upload `.fastq.gz` files to the Vidjil server.
Indeed, vidjil-algo takes into account the quality information in the output of the representative sequence.
When the base quality is not available, it is also possible to upload `fa.gz` files.
Note that vidjil-algo (and the Vidjil server) also accept uncompressed `.fastq` or `.fa` files
and even `.bam` files (but the added information of `.bam` files is not taken into account,
so uploading such files is not optimal).
## Local pre-filtering of large datasets
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