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Dear Developers, Thank you for providing such detailed documentation for the users. Being a novice to the Bioinformatics world, even I was able to install the S/w and execute bash workflow with ease. We recently procured Iontorrent genestudio S5 for our lab and did the first sequencing run using a Mock DNA mix containing 8 bacteria and 2 yeast (Zymobiomics, catno:D6306). We got around 45 million good-quality reads. Any recommendations or advice would be very much helpful in this regard. Many thanks
Mock_contigs_bacteria_metabin_stats.txt |
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Replies: 6 comments
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Hey @srisvs33 gald to hear that you found the documentation useful. Default settings are useful for the majority of the cases. If you want to get more complete bins you can try increasing the completeness metric. Furthermore, you can also try to manually curate your genomes using Automappa which is a tool developed by one of the students in our lab (@WiscEvan ). |
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Hi @Sidduppal . Thank you for your response. Actually sequenced Mock community DNA mix consists of 8 bacterial sp. ( Pseudomonas aeruginosa , Escherichia coli , Salmonella enterica , Lactobacillus fermentum, Enterococcus faecalis , Staphylococcus aureus ,Listeria monocytogenes ,Bacillus subtilis ) and 2 Yeast (Saccharomyces cerevisiae , Cryptococcus neoformans). It looks like Autometa splitting the genome bins into smaller ones even though they are actually from same species. I am not sure why it is the case. Is there any way to avoid this. Many thanks. Venkat |
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Hey @srisvs33 , thanks for providing additional information.
Feel free to let us know in case of further questions 😄 |
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Dear @Sidduppal Thank you for your suggestions, Increasing the length cutoff certainly helped to get more complete genomes (> 90%) for up to 4 bacterial species. Cheers |
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Dear @Sidduppal, sorry to bother you again. Another Quick query, is it possible to provide multiple assemblies for binning in Bash workflow? regards |
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As of yet, it's not possible to provide multiple assemblies to bash workflow, however, you can create a simple bash loop and do some string manipulation to achieve that. |
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Hey @srisvs33 , thanks for providing additional information.
Escherichia coli, Salmonella enterica and Enterococcus faecalis all belong to the same family, Enterococcaceae. There might be some problem in binning them correctly as they are closely related and there's higher chance of them resulting in split bins. If you look at the Mock_contigs_bacteria_metabin_stats.txt you'll see that the only bins which has good completeness (bin1) belongs to completely different phylum from all the other bins (ie. proteobacteria), this is what I was mentioning, that genomes belonging to different taxonomic groups bin out well.
Unfortunately, autometa is only for bacteria and archae, thus it won't bin t…