LXS

Non-eukaryotic data and input files?

3

Hi, This looks very useful but from all the examples it seems the package focuses mostly on eukaryotic omic data? I wanted to use this for bacterial genomes, to generate...

spades --isolate automatically applied?

1

https://github.com/rrwick/Unicycler/blob/69e712eb95c4b9f8a46aade467260260a9ce7a91/unicycler/spades_func.py#L226 ``` command = [spades_path, '-o', spades_dir, '-k', kmer_string, '--threads', str(threads)] if i == 0: # first k-mer command += ['--isolate'] ``` Based on the code, it seems like the...

I'd like to export the individual statistics from a `grouped_ggbetweenstats` analysis as a .csv or .xslx file, or any other format really. Ideally you'd get the individual `$caption_data`, `$subtitle_data`, `$pairwise_comparisons_data`...

Seawater and related media

1

Hi, Not an issue but a few questions on the seawater recipe and adding other related media. How was the existing "meerwasser" recipe made, or what was the reference? https://github.com/jotech/gapseq/commit/5d0aeafc3d40a0430aaed84b4f6eb9aba2549df6#diff-d82c35c23e1d05980fc5b6b31e9b25b406f669fdf8c34a76805931fc784ae6a4...

[FEATURE REQUEST] Expected output of test_genomes?

1

**Is your feature request related to a problem? Please describe.** I ran PGAP on the test genome (test_genomes-2022-12-13.build6494 MG37), but how do I check if the run behaviour was as...

Hi, was running the tutorial example: ``` $ python3 go_metacompass.py -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -1 tutorial/thao2000.1.fq -2 tutorial/thao2000.2.fq -l 150 -o tutorial/example1_output -t 30 --notimestamps ``` but it failed: ``` REFERENCE genome...