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Oct 18, 2021
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add nanopore to ebi submissions #3145

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34 changes: 18 additions & 16 deletions qiita_pet/support_files/doc/source/gettingstartedguide/index.rst
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Expand Up @@ -281,22 +281,24 @@ In order to submit your data to EBI, certain fields are required in your prepara

For all valid values for instrument_model per platform, view the values in the table below:

+-----------------+----------------------------------------------------------------------------------------------------------+
| Platform | Valid instrument_model options |
+=================+==========================================================================================================+
| ``LS454`` | ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, |
| | ``454 GS Junior`` or ``unspecified`` |
+-----------------+----------------------------------------------------------------------------------------------------------+
| ``Illumina`` | ``HiSeq X Five``, ``HiSeq X Ten``, ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``, |
| | ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``, |
| | ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``, |
| | ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``, |
| | ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or `unspecified`` |
+-----------------+----------------------------------------------------------------------------------------------------------+
| ``Ion_Torrent`` | ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL`` |
+-----------------+----------------------------------------------------------------------------------------------------------+
| ``PacBio_SMRT`` | ``PacBio RS``, ``PacBio RS II``, ``Sequel ``, ``Sequel II`` |
+-----------------+----------------------------------------------------------------------------------------------------------+
+---------------------+----------------------------------------------------------------------------------------------------------+
| Platform | Valid instrument_model options |
+=====================+==========================================================================================================+
| ``LS454`` | ``454 GS``, ``454 GS 20``, ``454 GS FLX``, ``454 GS FLX+``, ``454 GS FLX Titanium``, ``454 GS Junior``, |
| | ``454 GS Junior`` or ``unspecified`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``Illumina`` | ``HiSeq X Five``, ``HiSeq X Ten``, ``Illumina Genome Analyzer``, ``Illumina Genome Analyzer II``, |
| | ``Illumina Genome Analyzer IIx``, ``Illumina HiScanSQ``, ``Illumina HiSeq 1000``, |
| | ``Illumina HiSeq 1500``,, ``Illumina HiSeq 2000``, ``Illumina HiSeq 2500``, ``Illumina HiSeq 3000``, |
| | ``Illumina HiSeq 4000``, ``Illumina MiSeq``, ``Illumina MiniSeq``, ``Illumina NovaSeq 6000``, |
| | ``NextSeq 500``, ``NextSeq 550``, ``Illumina NovaSeq 6000`` or ``unspecified`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``Ion_Torrent`` | ``Ion Torrent PGM``, ``Ion Torrent Proton``, ``Ion Torrent S5``, ``Ion Torrent S5 XL`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``PacBio_SMRT`` | ``PacBio RS``, ``PacBio RS II``, ``Sequel``, ``Sequel II`` |
+---------------------+----------------------------------------------------------------------------------------------------------+
| ``Oxford_Nanopore`` | ``GridION`` |
+---------------------+----------------------------------------------------------------------------------------------------------+


Required fields for pre-processing target gene data
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1 change: 1 addition & 0 deletions qiita_ware/ebi.py
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Expand Up @@ -113,6 +113,7 @@ class EBISubmission(object):
'NEXTSEQ 500',
'NEXTSEQ 550',
'UNSPECIFIED'],
'OXFORD_NANOPORE': ['GRIDION'],
'PACBIO_SMRT': ['PACBIO RS',
'PACBIO RS II',
'SEQUEL',
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