BOLDigger

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Include BOLD API extra data for corrected list of top hits?

5

Hello! I've been using BOLDigger for a while and I am so appreciative to have this tool at my fingertips! I'm recently exploring the option to generate a top hit...

myoung02

ID description

3

Hi Dominik, I'm working with BOLDigger v.2.0.3 (and boldigger-cline v.1.0.0) and have the issue that the "ID" in the results file starts with the greater-than (">") symbol (inherited from the...

SaschaKrenek

- Wrong number of columns passed to the id engine code for ITS and rbcl, will fix soon

DominikBuchner

Ubuntu: rbcl fasta file run error

4

Hi, I'm using the BOLDigger v1.5.6 with Python 3.8 and there was an error: Traceback (most recent call last): File "/home/yao/.local/bin/boldigger", line 8, in sys.exit(main()) File "/home/yao/.local/lib/python3.8/site-packages/boldigger/__main__.py", line 108, in...

Canxis

Limit PySimpleGUI requirement to version 4

1

[PySimpleGUI 5 is out, but is now closed-source and subscription-based](https://news.ycombinator.com/item?id=39369353) Although the subscription is free for non-commercial users, which includes most of us, it requires you to acquire a free...

hjarnek

Assigning BIN to top hits

6

Getting Barcode Index Numbers (BINs) could be useful for certain analyses as a extra source of information, especially in datasets with many undescribed species. I imagine the procedure for assigning...

gjdury

Filter possible NUMTS from BOLDigger assignments

1

It is possible that in the metabarcoding amplification process not only the mitochondrial gene [but also nuclear copies of that gene were amplified](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000834). And they can lead to false positive...

AlvaroFueyo

I modified jamp_hit.py in a way that is compatible (as far as I tested) with digger_hit when used with boldigger-cline. I did not test it with the GUI. This version...

gjdury

Passing literal html to 'read_html' is deprecated and will be removed in a future version.

1

Hello @DominikBuchner, Thank you for creating this awesome tool! Just to note that I've received the following warning when running BOLDIGGER via the command line (`boldigger-cline ie_coi`). It seems to...

gjeunen

BOLD Not Responding: Attempting Retry

16

Hi, I run the rbcl analysis on BOLDigger with 3 batch size (since it is reported that it should be less than 5). However, I encountered an error with BOLD...

anilorun