Skip to content
Search for a set of compatible indexes for your sequencing experiment
R
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
www
.gitignore
LICENSE
README.md
checkMyIndex.r
global.r
index24-i5.txt
index24-i7.txt
index96_UDI-i5.txt
index96_UDI-i7.txt
inputIndexesExample.txt
server.r
ui.r

README.md

checkMyIndex

Search for a set of compatible indexes for your sequencing experiment according to:

  • the number of samples
  • the desired multiplexing rate (i.e. number of samples per pool/lane)
  • the constraint on the indexes (none, use each one or each combination only once)

Input indexes file

The list of the available indexes must be stored in a text file containing two tab-separated columns (without header): index ids are in the first column and the corresponding sequences in the second. inputIndexesExample.txt is an example of such a file and can be used to test checkMyIndex. For dual-indexing sequencing experiments the user needs to provide two files: the first one for the indexes 1 (i7) and the second for the indexes 2 (i5). index24-i7.txt and index24-i5.txt are available to test the research of compatible dual-indexes. Moreover, two files index96_UDI-i5.txt and index96_UDI-i7.txt are available to test the application in a Unique Dual-Indexing (UDI) context.

Shiny application

Public website

Click here to use the shiny interface of checkMyIndex.

Locally

If both shiny and shinyjs R packages are already installed, one can use the application locally running the two following lines in R:

library(shiny)

runGitHub("PF2-pasteur-fr/checkMyIndex", launch.browser=TRUE)

Rscript command line

checkMyIndex can be executed calling checkMyIndex.r with Rscript. As checkMyIndex.r sources global.r, both files must be placed in the same directory. Here are 4 examples using either inputIndexesExample.txt or index24-i7.txt and index24-i5.txt:

  • List of 9 indexes for 9 samples distributed on 3 lanes with the four-channel Illumina chemistry:

Rscript checkMyIndex.r --inputFile7=inputIndexesExample.txt -C 4 -n 9 -m 3

  • List of 12 indexes for 12 samples distributed on 4 lanes with the four-channel Illumina chemistry using each lane combination only once:

Rscript checkMyIndex.r --inputFile7=inputIndexesExample.txt -C 4 -n 12 -m 3 -u lane

  • List of 12 indexes for 12 samples distributed on 4 lanes with the two-channel Illumina chemistry using each index only once:

Rscript checkMyIndex.r --inputFile7=inputIndexesExample.txt -C 2 -n 12 -m 3 -u index

  • List of 24 dual-indexes for 24 samples distributed on 2 lanes with the two-channel Illumina chemistry:

Rscript checkMyIndex.r --inputFile7=index24-i7.txt --inputFile5=index24-i5.txt -C 2 -n 24 -m 12

The help page of the script can be displayed running the following command:

Rscript checkMyIndex.r --help

Requirements

Here is the list of the R packages needed to run checkMyIndex:

  • shiny and shinyjs to run the shiny application locally

  • optparse to interpret the input parameters when using the Rscript command line

  • parallel to speed up the calculations

One can install each of these packages running install.packages(packageName) in R.

Illumina chemistry

Illumina has developed three types of chemistry: the four-channels for the HiSeq and MiSeq sequencing devices, the two-channels for the NovaSeq, NextSeq and MiniSeq devices and the one-channel for the iSeq 100 device. With the four-channel chemistry, a red laser detects A/C bases and a green laser detects G/T bases and the indexes are compatible if there is at least one red light and one green light at each position. With the two-channel chemistry, G bases have no color, A bases are orange, C bases are red and T bases are green and indexes are compatible if there is at least one color at each position. Note that indexes starting with GG are not compatible with the two-channel chemistry. With the one-channel chemistry, compatibility cannot be defined with colors and indexes are compatible if there is at least one A or C or T base at each position. Please refer to the Illumina documentation for more detailed information on the different chemistries.

News

  • Version 1.0.1: update of the user interface with shinyjs
  • Version 1.0.2: deal with the new Illumina unique dual-indexes (UDI)

About checkMyIndex

This tool has been developed at the Biomics pole of the Institut Pasteur by Hugo Varet (hugo.varet@pasteur.fr) and an Application Note describing it has been published in 2018 in Bioinformatics. Please note that checkMyIndex is provided without any guarantees as to its accuracy.

You can’t perform that action at this time.