Chromosome Submission

The submission route for chromosomes depends on a number of factors, for example whether or not there is annotation associated with the sequences and on the availability of an AGP file containing the chromosome assembly details. Select the appropriate case for your submission. For submission of complete genomes please refer to sections C or D, depending on availibility of annotation. Please do not hesitate to contact us if you feel your case is not covered below.

 

            A) Chromosomes with AGP file available, without annotation

            B) Chromosomes with AGP file available, with annotation

            C) Chromosomes with no AGP available, without annotation (including complete genomes)

            D) Chromosomes with no AGP available, with annotation (including complete genomes)

          

A) Chromosome with AGP file available, without annotation

If you have an AGP which describes your chromosomes, we request you to submit the contigs and/or scaffolds. After the contigs and/or scaffolds submission, please use the Webin box to upload the AGP file for us to construct the corresponding chromosome. The AGP file must pass the NCBI AGP validator.  Once you have submitted the contigs and/or scaffolds and also uploaded the AGP file into the Webin box, please contact datasubs@ebi.ac.uk to let us know that the submission is complete stating the Webin box number (era-drop-NNN number).

 

 

B) Chromosomes with AGP file available, with annotation

If you have an AGP which describes your chromosomes, we request you to submit the contigs and/or scaffolds. After the contigs and/or scaffolds submission, please use the Webin box to upload a) an EMBL file containing the annotation for the chromosome (for annotation guidelines please visit here) and b) an AGP file for us to construct the corresponding chromosome. The AGP file must pass the NCBI AGP validator

Once you have submitted the contigs and/or scaffolds, uploaded the AGP file and the EMBL annotation file into the Webin box, please contact datasubs@ebi.ac.uk to let us know that the submission is complete stating the Webin box number (era-drop-NNN number).

 

 

C) Chromosomes with no AGP, NO annotation

If you have built your chromosomes, you don’t have the AGP file and contigs to submit, please follow one of the options below depending on the presence of gaps and if you can provide assembly gap information:

i)  If there are no gaps, the submission should be made via ENA's interactive Webin system, using Entry upload. For this, log into your Webin ENA account here. On the left hand menu select "New Submission" and then select " Entry upload” at the end of the page. Follow the instructions on the screen.

ii) If there are gaps but you cannot provide assembly_gap feature annotation (details here), you are requested to provide a minimum gap length which we need to consider to build default assembly_gap feature for your genome. For example if you say your minimum gap length should be 20, we will create assembly_gap feature for all the stretches of NNNNNs with the length equal and more than 20.

The submission should be made via ENA's interactive Webin system, using Entry upload. For this, log into your Webin account here. On the left hand menu select "New Submission" and then select " Entry upload” at the end of the page. Follow the instructions on the screen. Please provide minimum gap length by putting a note in “Comments” box (last Webin submission page) “The minimum gap length should be N”.

iii) If there are gaps and you can provide assembly gap information using the assembly_gap feature (details here), please include this information as genome annotation and follow the instruction in section D (chromosomes with NO AGP available, with annotation)

 

 

D) Chromosomes with no AGP available, with annotation.

If you have built your chromosomes, you don’t have the AGP file and contigs to submit and you have annotation with/without assembly_gap feature annotation, the submission should be done always via ENA's interactive Webin system. For annotation guidelines including the assembly_gap feature, please visit here

First, prepare an EMBL file with the sequences and the associated annotation. If there are gaps in your genome and you have assembly gap information, annotate your records with the assembly_gap feature (details here). If there are gaps but you do not have the assembly_gap information feature, you need to provide a minimum gap length which we need to consider to build the default assembly_gap feature for your genome. For example if you say your minimum gap length should be 20, we will create assembly_gap feature for all the stretches of NNNNNs with the length equal and more than 20. Please include this information in the Curator Comments box (last Webin submission page) saying“Chromosomes with no AGP, with annotation” and “The minimum gap length should be N”. The minimum gap length should be N”.N is the number we will consider for minimum gap length.

Once the EMBL file is complete, to submit via Webin log into your Webin account here. On the left hand menu select "New Submission" and then select " Entry upload” at the end of the page. Follow the instructions on the screen.