Taylor Reiter

Exporting manubot manuscript to Rmd

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Hello! I recently used manubot to draft a collaborative document, it was a wonderful experience -- thank you for generating such a great tool! I now find need to export...

Point to "assembly_summary.txt" instead of downloading files

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Hello! I am using snakemake to parallelize the download of ~100k genomes from RefSeq using biomartr. In doing so, I am running one download Rsession for each genome that I...

metagenome assembly graphs are really big. But subgraphs, either produced with a genome or gene query, are much smaller. It would be really cool if we had a tutorial or...

does protein query support degenerative amino acid alphabets?

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and if it does not, would it be easy for that to be implemented? I haven't finished evaluating the sensitivity/specificity of protein queries as is, but just wondering if e.g....

can we convert the cDBG to GFA format with the current output files from spacegraphcats?

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I'm wondering if we can convert the current bcalm output by spacegraphcats to gfa. These are the current output files in `*_k31`: ``` bcalm.inputlist.txt bcalm.unitigs.db cdbg.gxt contigs.mphf reads.bgz.index bcalm.log.txt bcalm.unitigs.fa.sig...

When `extract_reads` is run as part of a larger workflow, it's sometimes hard to figure out the best strategy to use to encode the 1:many problem (one sample in, many...

Im watching some talks this morning from a DePaul University College of Computing and Digital media speaker series. The one I’m watching right now is by Ben Langmead and covers...

ProtectedOutputException: Write-protected output files for rule bcalm_catlas_prepare_input: GCF_000765235.1_k31/bcalm.unitigs.db

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``` ProtectedOutputException in line 199 of /home/tereiter/github/2020-ibd/.snakemake/conda/7218b88cfb8b4e4 e84f86d335f04be9e/lib/python3.8/site-packages/spacegraphcats/conf/Snakefile: Write-protected output files for rule bcalm_catlas_prepare_input: GCF_000765235.1_k31/bcalm.unitigs.db File "/home/tereiter/github/2020-ibd/.snakemake/conda/7218b88cfb8b4e4e84f86d335f04be9e/lib/python3.8/ site-packages/snakemake/executors/__init__.py", line 136, in run_jobs File "/home/tereiter/github/2020-ibd/.snakemake/conda/7218b88cfb8b4e4e84f86d335f04be9e/lib/python3.8/ site-packages/snakemake/executors/__init__.py", line 441, in run File...

Which is not currently a problem, but as the links may break at any time, I wanted to open an issue about it.

Annotating the catlas

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relevant to #309 I've been working on annotating catlases. In this use case, I built a "metapangenome" graph. I did a genome query (_R. gnavus_) in 605 gut microbiome metagenomes,...