BUSCO_phylogenomics
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jamiemcg
BUSCO Phylogenomics | Utility script to construct species phylogenies using BUSCO proteins
Having "`*run_*`" in the BUSCO output directory name causes an error (e.g. BUSCO5_rerun_XYZ_output) https://github.com/jamiemcg/BUSCO_phylogenomics/blob/0589f6ce883c3ebfa3b7521339d8caaf7f8bc526/count_buscos.py#L44-L49 (It looks for BUSCO sequences in the "logs" directory as it thinks it is the run...
Sometimes, recovered BUSCOs are flagged as being "fragmented" even though they are full length (due to divergence from ref db). Add an optional flag "--include-fragmented" for these sequences to be...
Add this: ``` print("\t".join(["\t"] + [busco_sample_name for busco_sample_name in busco_sample_names])) ``` Here: https://github.com/jamiemcg/BUSCO_phylogenomics/blob/0589f6ce883c3ebfa3b7521339d8caaf7f8bc526/count_buscos.py#L134-L145
Hello, I am running into an issue with a 47 genomes, 874182 columns dataset. When I attempt to run this pipeline I get an error from IQTree that shuts down...
