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vidjil
vidjil
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fa345b44
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fa345b44
authored
Feb 12, 2021
by
Mathieu Giraud
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doc/workflow.md: workflow and file formats, draft
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# 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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