Taylor Reiter

Adding more information to include examples! The RMarkdown might look something like this: ``` --- bibliography: references.json title: My document output: pdf_document --- ## Introduction Historically, this has led to...

Andddd in posting this update, I realized that replacing ``` --- bibliography: references.json title: My document output: pdf_document --- ## Introduction Historically, this has led to a thing that we...

Thank you! In case others find it useful, here is the snakefile I would use to down the accessions I'm interested in: `Snakefile`: ``` import pandas as pd import re...

Hello @rob-p! I was wondering if there have been any updates on the fusion/detection of spanning reads problem. I'm about to embark on a project to process many bacterial transcriptomes...

I guess I could make a gather database that contains all of the queries, and then run the original sample against this database to get the approx. portion that is...

I see how this could be beneficial for running sgc from the command line, but I think it makes it more complicated (especially to debug) when running sgc from within...

Hi Tamer -- I recently wrote a script to do something like that: https://github.com/dib-lab/2020-ibd/blob/master/scripts/cdbg_to_pieces.py Usage: ``` python -m spacegraphcats build conf.yml cdbg_to_pieces.py cdbg_dir catlas_dir ``` it outputs `cdbg_to_pieces.csv` in the...

ok great, thanks. I'm increasingly thinking of ways to better integrate with other people interested in metagenome assembly graphs, and I think gfa is a pretty standard format that wouldn't...

@ctb's response in slack: yep. bcalm and extract_reads are the only ones that COULD take advantage of multiple jobs, and bcalm isn’t configured appropriately yet but may take advantage of...

``` rule spacegraphcats_multifasta: input: queries = expand('outputs/gather_matches_loso_prokka/{gather_genome}.ffn', gather_genome = GATHER_GENOMES), conf = "inputs/sgc_conf/{library}_r1_multifasta_conf.yml", reads = "outputs/abundtrim/{library}.abundtrim.fq.gz", sig = "outputs/vita_rf/at_least_5_studies_vita_vars.sig" output: "outputs/sgc_genome_queries/{library}_k31_r1_multifasta/query-results.csv" params: outdir = "outputs/sgc_genome_queries", #out = lambda wildcards: wildcards.library...