ONT compatibility

[fcamara7]

Hi Diego,

Over here at the CNAG, as you know, we currently assemble genomes using ONT technology and I have had a bit of trouble getting your report to work for us. One issue we have is that since we have a "collapsed" assembly merqury only produces three st.png files and your python script is expecting four.

Thanks for helping us with this when you have time!

---

Our yaml is below.

This is the yaml file for generating the ERGA Assembly Report (EAR) using the make_EAR.py script

Please complete the required information pointed as <Insert ...>

The file [example]rCarCar2_EAR.yaml contains an example of a completed yaml file

GENERAL INFORMATION

ToLID: fValHis Species: Valencia hispanica Sex: unknown # for example: XX, XY, ZZ, ZW, unknown, NA... Submitter: Francisco Camara Ferreira Affiliation: CNAG Barcelona Tags: ERGA-BGE # valid tags are ERGA-Pilot, ERGA-BGE, ERGA-Satellite

SEQUENCING DATA

DATA:

• ONT: 74x
• Illumina: 83x
• OmniC: 70x

GENOME PROFILING DATA

PROFILING: GenomeScope: version: 2.0 results_folder: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/s02.2_p01.1_preprocess_illumina_reads/genomescope2_k21

ASSEMBLY PIPELINE

CONTIGGING: nextdenovo: version: 2.5.0 collapsed: gfastats--nstar-report_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/s03.2_p02.1_nextdenovo/nextdenovo.assembly.gfastats.txt busco_short_summary_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s03.2_p02.1_nextdenovo/busco/nextdenovo.assembly.short_summary.txt merqury_folder: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s03.2_p02.1_nextdenovo/merqury/nextdenovo.assembly

hypo: version: 1.0.3 collapsed: gfastats--nstar-report_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/s04.2_p03.2_polishing/hypo/nextdenovo.assembly.hypo1.gfastats.txt busco_short_summary_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s04.2_p03.2_polishing/busco/nextdenovo.assembly.hypo1.short_summary.txt merqury_folder: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s04.2_p03.2_polishing/merqury/nextdenovo.assembly.hypo1

purge_dups: version: 1.2.6 collapsed: gfastats--nstar-report_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/s05.1_p04.1_run_purgedups/flye.assembly.hypo1.purged.gfastats.txt busco_short_summary_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s05.3_p04.2_run_purgedups/busco/nextdenovo.assembly.hypo1.purged.short_summary.txt merqury_folder: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/s05.3_p04.2_run_purgedups/merqury/nextdenovo.assembly.hypo1.purged_complete

SCAFFOLDING: YaHS: version: 1.2a collapsed: gfastats--nstar-report_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/curation/yahs_scaffolding/fValHis_yahs_scaffolds_final.gfastats.txt busco_short_summary_txt: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/yahs_scaffolding/busco/fValHis_yahs_scaffolds_final.short_summary.txt merqury_folder: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/evaluations/yahs_scaffolding/merqury/fValHis_yahs_scaffolds_final pretext_FullMap_png: /scratch_isilon/groups/assembly/data/projects/BGE/fValHis/assembly/curation/hic_remap/out_fValHis_yahs_scaffolds_final/snapshots/three_wave_blue_green_yellow/assembly_mq40.fValHis_yahs_scaffolds_final_FullMap.png

[diegomics]

Hi @fcamara7 I just came back. I will look into this ;)

[diegomics]

Hi @fcamara7 please check the updated script, let me know if it's working

[fcamara7]

Thanks @diegomics !! It seems to work just fine now! I will show it to Tyler tomorrow and I will get back to you if there are any further issues but I think it is fine now. Thanks for acting on this so quickly! :)