Comments (1)
Hi Max,
Thanks for reaching out with detailed information.
- (1) It's expected to be either circular or linear. For more information, please see here https://github.com/Kinggerm/GetOrganelle/wiki/FAQ#why-does-getorganelle-generate-a-circular-genome-or-not-for-embplant_nrfungus_nr.
- (2&3&4). A shorter length is problematic. It results from the conservative shortcut that the current GetOrganelle version took, which only assigns the unique label to only one contig, which should work with a complete circular result but not the other way around. I have improved this in the next version (available at the intermediate_graph branch); however, it will take a while for me to test the new version comprehensively before releasing it.
I believe you are doing step 4 manually and correctly. Thefiltered*fastg
file can be helpful too. I usually check it rather than the original fastg file. You can also do step 4 using a semi-manual (combining "slim_graph.py") approach. - (5) Probably using
evaluate_assembly_using_mapping.py
and/or building a phylogeny as you did. - (6) Yes and no. You can input single-end short read using
-u
. It's not compatible mainly because using long error-prone reads alone can be problematic. I'm developing another tool (Traversome) for combining short- and long- reads to solve a more generic problem. - (7) It depends on how diverged the sequences are. If it were plastomes within angiosperm scope, which evolved slowly, I would say no influence at all. I don't know much about animal ITS. But you can easily confirm this by using a more related label.
Extra tip, given the depths & the graph, you can speed up each run by using even a larger -w
and fewer rounds.
Best,
Jianjun
from getorganelle.
Related Issues (20)
- ERROR: slimming the pre-assembled graph failed
- AssertionError: Invalid characters (e.g. space, non-ascii) for SPAdes in path: /home/ruizhang/zhaoliaocheng/Viburnum cpDNA/LYL47/plastome_output
- 2023-05-24 14:15:33,428 - INFO: Round 9: 10081574/10081574 AI 89119 AW 2714392 2023-05-24 14:15:33,428 - INFO: No more reads found and terminated ... 2023-05-24 14:16:02,153 - INFO: Extending finished. HOT 1
- incomplete assembly graph HOT 2
- Discrepancy between get_organelle_from_reads and summary_get_organelle_output logs HOT 1
- Set Startingpoint of Cicular Mitochondrial Genome HOT 2
- conda install error: conda version 23.5.0 too high HOT 2
- Please explain the output - multiple fasta HOT 1
- assembly_graph.fastg finished with no target organelle contigs found! HOT 7
- empty filtered paired HOT 2
- Problems with chloroplast genome assembly stagnation HOT 4
- Invalid information provided HOT 1
- dogged request of help with Invalid version spec: =2.7 HOT 5
- ERROR: slimming the pre-assembled graph failed HOT 1
- not able to to run "summary_get_organelle_output.py" and "IndexError:list out of range" HOT 1
- I have problem with running getorganelle in cluster HOT 1
- Crashes while running GetOrganelle when I try to use all raw reads HOT 2
- Slimming failed and no valid assembly graph found HOT 6
- How to jugde circular? HOT 1
- How to provide multiple sets of paired-reads? HOT 1
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