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discoAnt

  • version 07082022
  • tested on conda v4.12.0

Updates in v2.1

  • optional primer site based filter
  • report: includes statistics for the FASTA files and number of known and novel transcripts
  • edits to the transcript file output for compatibility with IsoMix

Prepare FASTA files in a folder

All the sample files (pass-reads only) should be in FASTA format (.fa)

Setting up discoAnt

  1. Downloading the workflow with git clone

  2. Downloading relevant reference file and creating a conda environment
    cd discoAnt
    bash discoAnt_setup.sh

  3. Running a test script to check installation
    conda activate discoAnt
    bash discoAnt_v2_SIRV_test.sh

  4. Update discoAnt_params.txt with gene info and paths to relevant folders before running the workflow with the data set of your choice
    conda activate discoAnt.env
    bash discoAnt_v2.1.sh

Refer to the sample submission scripts for running the pipeline on a HPC cluster.

Workflow

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