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README.md  view on Meta::CPAN

   - [wgs2ncbi.ini](share/wgs2ncbi.ini) - the main configuration file, in which you 
     specify the locations of the input files and output directories. In addition, here
     you will specify the prefixes for the identifiers that will be inserted in the 
     feature tables and various parameters for what to filter on. The file is well 
     documented with comments.
   - [info.ini](share/info.ini) - a file with key/value pairs whose contents will be 
     inserted in the FASTA headers of the sequence files. These key/value pairs have to
     do with the organism that was sequenced, such as the taxon name, its sex, its
     developmental stages, what tissues were sampled, and so on.
   - [adaptors.ini](share/adaptors.ini) - this is a file that contains the coordinates 
     of sequence fragments that NCBI considers inadmissible. What will happen over the
     course of your submission is that NCBI will scan your sequence data for suspicious
     sequence fragments. These might be adaptor sequences of various sequencing platforms,
     and fragments that NCBI thinks might be contaminants. Hence, during your first pass
     it is more or less impossible to get the values right in this file: this part will
     be an iterative process where you blank out parts of your data that NCBI really will
     not accept. Start out with an empty file, and populate it based on the feedback you
     will get, making sure you follow the same syntax as the provided example file.
   - [products.ini](share/products.ini) - this is a file that contains mappings from 
     (parts of) the gene names that you assigned during the annotation process to names
     that NCBI will accept. Again, this is impossible to predict during the first pass:
     you will get feedback on which names NCBI doesn't like (for example because there are
     things in the names that look like database identifiers, organism names, molecular
     weights, etc.) and in this file you map these to allowed names.

README.md  view on Meta::CPAN

- the genome assembly, i.e. the large FASTA file, is chopped up into smaller FASTA files.
  All but the last of these output files will contain as many FASTA records as specified
  by [chunksize](https://github.com/naturalis/wgs2ncbi/blob/master/share/wgs2ncbi.ini#L57)
  with the last one containing the remainder. If all your contigs are longer than the
  [minlength](https://github.com/naturalis/wgs2ncbi/blob/master/share/wgs2ncbi.ini#L60)
  then the number of files thus produced will be the number of contigs, divided by 
  `chunksize`, rounded up to the nearest integer. However, contigs smaller than
  `minlength`, if you have them, will be omitted, as NCBI won't accept these.
- the FASTA data that will be written will have any stretches specified in
  [adaptors.ini](share/adaptors.ini) replaced with `NNNs`. These will be sequence 
  fragments that NCBI will specify as inadmissible because they might be sequence adaptors 
  (i.e. vendor-specific synthetic DNA) or contaminants.
- the FASTA files will have the `.fsa` file extension, as required by `tbl2asn`.  
- the annotations from the GFF3 file, pre-processed in the previous step, will be written
  out as feature tables (required extension: `.tbl`). There will be as many `.tbl` files 
  as there are `.fsa` files.
- any gene annotations that have introns that are shorter than
  [minintron](https://github.com/naturalis/wgs2ncbi/blob/master/share/wgs2ncbi.ini#L67)
  will be converted to pseudogenes, as NCBI does not believe these could be real.
- any gene product names that are unacceptable to NCBI, and for which you have provided 
  a mapping in [products.ini](share/products.ini), will be mapped to the names