Diploid Assembly Submission to NCBI

NCBI now accepts diploid genome submissions! This repository contains a collection of scripts to aid you in generating the placement file required by NCBI. Details can be found here. Refer to the Arabidopsis thaliana assembly from Chin et al. 2016 as you prepare your FALCON-Unzip assembly for submission to NCBI.

Placement File

The placement file for an unscaffolded assembly has the following fields:

1. alt_asm_name: name of the assembly-unit that includes the alternate scaffold.
2. prim_asm_name: name of the assembly-unit on which the alternate scaffold is being placed. Expected to be 'Primary Assembly' in most cases.
3. alt_scaf_name: name of the alternate scaffold being placed
4. parent_type: type of object on which the alternate scaffold is being placed, either CHROMOSOME or SCAFFOLD
5. parent_name: name of the object on which the alternate scaffold is being placed (can be either a chromosome or a scaffold)
6. ori: orientation of the alignment, '+', '-', 'b'(mixed)
7. alt_scaf_start: start of the placement on the alternate scaffold (in 1 base coordinates)
8. alt_scaf_stop: end of the placement on the alternate scaffold (in 1 base coordinates)
9. parent_start: start of the placement on the parent sequence (in 1 base coordinates)
10. parent_stop: end of the placement on the parent sequence (in 1 base coordinates)
11. alt_start_tail: number of bases at the start of the alternate scaffold not involved in the placement
12. alt_stop_tail: number of bases at the end of the alternate scaffold not involved in the placement

Example Placement File

Refer to AthalPlacementFile.txt in this repository for the Arabidpsis thaliana file.

Scripts to generate placement files

Either of the following scripts can be used to generate a placement file.

nucmer2ncbiPlacement.py

Python script written by Sarah Kingan that generates placement file for diploid genome assembly. This script operates on a directory containing "coords" files created from nucmer alignments between each haplotig and its associated primary contig. The commands to generate "coords" files can be found within script on lines 23-43.

generate_placement.py

python script written by Jason Chin that performs nucmer alignments, generates coords file, and created placement file for NCBI submission. Dependencies include FastaReader.py and mummer.

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