/assembler-scripts

Scripts I used to run assemblers for the 2021 benchmarking study

Primary LanguageShell

Assembler-scripts

Scripts I used to run assemblers for the 2021 benchmarking study

Runing assemblers

How to use

  1. Modify runAllSubsamples.sh:
    • Variables at top hold the location of the files
    • -d parameter is the read depths testing
    • -p parameter is the prefix to use for file name
  2. bash source/runAllSubsamples.sh

Adding an assembler

  1. Modify runAssemblers.sh to recognize the runAssemblerName.sh script
    • Line 84 add your assembler to the list of recongnized assemblers (valdAsmbStr variable)
    • Line 586 Add an if statement to check for your assembler
  2. Adds script to run your assembler in the source/assembler directory
    • If copying assembler script from source/assembler
    • Assembler call: Section 4
    • Get user arguments: Section 2

Other usefull scripts (in extra-scripts)

  1. metaQuastAddBlank.sh adds a blank entry for replicates that were detected less than 12 times
    • Use: metaQuastAddBlank.sh prefix--metaStats-combined.csv
    • Can be changed from 12 to any other number by changing numIdInt=12 paramter on line
    • Is needed to avoid ggplot error of unequal numbers of replicates for each sequence
    • Will not detect refences that were completey missed

Non-scripted steps:

For MetaQuast, if you are working with both plasmids and chromosomes, you will have to manually mark plasmids and chromosomes in the MetaQuast csv file.

R scripts

Building graphs

The R scripts are designed for the species used in our benchmarking study.

  1. Chromosome pomoxis data:
    • Rscript pomoxisGraph.r
  2. Plasmid pomoxis data:
    • pomoxisGraph.r
  3. Metaquas data:
    • Rscript metaQuastIsolet.r
  4. time and memory data:
    • Rscript timeGraphs.r

Statistics for subsamples

Rscript r-scripts/subsampleStats.r