How to use the scipt "summary_get_organelle_output.py? about getorganelle HOT 3 CLOSED

The input of "summary_get_organelle_output.py" is the output folder(s), (after the flag "-o" in your "get_organelle_from_reads.py" command). e.g. you have multiple samples finished with

get_organelle_from_reads.py -1 sample1_1.fq.gz -2 sample1_2.fq.gz -t 1 -o sample1-plastome -F embplant_pt -R 10
get_organelle_from_reads.py -1 sample2_1.fq.gz -2 sample2_2.fq.gz -t 1 -o sample2-plastome -F embplant_pt -R 10
get_organelle_from_reads.py -1 sample3_1.fq.gz -2 sample3_2.fq.gz -t 1 -o sample3-plastome -F embplant_pt -R 10

Then, you can summarize those results with

summary_get_organelle_output.py  sample_1-plastome sample_2-plastome sample_3-plastome -o plastome_run_stat.tab

or

summary_get_organelle_output.py sample*-plastome -o plastome_run_stat.tab

from getorganelle.

Thanks for posting this! I just realize that I forgot to update the description/termination for "evaluate_assembly_using_mapping.py". It's outdated and inaccurate. Now I have correct the description in the code.

It SHOULD BE "Matched: 375.33±66.39 (375.33±66.39)", NOT "Aligned: 375.33±66.39 (375.33±66.39)", meaning the mean and standard deviation of matched bases per site (depth/coverage) of the mapping alignment.
The format can be described as
Matched: global_depth_mean±global_depth_stdev (contig_depth_mean±contig_depth_stdev)

Refer to Reads mapping to evaluate plastome assemblies in the manuscript (https://www.biorxiv.org/content/10.1101/256479v4.full). The biorxiv version was actually updated again with minor clarification in our submission version to the journal, but the idea is the same.

from getorganelle.

Thank you very much. I can successfully run the script:summary_get_organelle_output.py. Thank you for your explanation of the Matched: 375.33±66.39 (375.33±66.39).

from getorganelle.