From 2d95f311e1ef38c5ea1ae73055fcbfb096d9dd0f Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Tue, 3 Sep 2024 11:09:40 -0400 Subject: [PATCH] nix example --- paper/mra.md | 41 ----------------------------------------- 1 file changed, 41 deletions(-) diff --git a/paper/mra.md b/paper/mra.md index d038120..32563c4 100644 --- a/paper/mra.md +++ b/paper/mra.md @@ -132,47 +132,6 @@ To download the accessions in the tsv files, there is an included script `downloadKalamari.pl` that accesses GenBank with its software, Entrez Direct [@kans2016entrez]. Accessions reside in the GitHub repo, at . -## Example Usage - -Kalamari can be used where most metagenomic analyses are used. -Most commonly, we use Kalamari to customize databases for Kraken1 [@wood2014kraken] or Kraken2 [@wood2019improved]. -Building the Kraken database has been implemented in `buildKraken1.sh` -and in `buildKraken2.sh`. -However, other descriptions for building databases such as for BLAST+ [@camacho2009blast] -or Mash [@ondov2016mash] can be found in the documentation. - -For single genomes, a metagenomic database is useful for quality control because -a user can have a null hypothesis that the sample is a metagenomic sample with a singular taxon. -An alternate hypothesis of contamination can be supported when conflicting taxa are detected by the database. -Therefore, a data scientist could use Kalamari as a way to detect contamination. -For metagenomes, the database is useful as intended, to detect which taxa are present in a sample. - -A more concise example is shown - -```bash -# Set up the environment -export PATH=$PATH:$(realpath kalamari/bin) -# Understand where the output files are -KALAMARI_VER=$(downloadKalamari.pl --version) -OUTDIR="kalamari/share/kalamari-$KALAMARI_VER" - -# after installing Kalamari -downloadKalamari.sh -# => files are now in $OUTDIR/kalamari -buildTaxonomy.sh -# => files are now in $OUTDIR/taxonomy -filterTaxonomy.sh -# => files are now in $OUTDIR/taxonomy/filtered - -# Load kraken1 into the environment -buildKraken1.sh -# => files are now in $OUTDIR/kalamari-kraken - -# Unload Kraken1 and then load Kraken2 into the environment -buildKraken2.sh -# => files are now in $OUTDIR/kalamari-kraken2 -``` - ## Acknowledgements This work was made possible through support from the Advanced Molecular Detection (AMD) Initiative at the Centers for Disease Control and Prevention.