btv_sequencing_2

This is a modified version of the btv_sequencing pipeline from the Stenglein Lab at CSU. It was built for this purpose but has since been updated.

It is currently intended for use with paired-end, Illumina short-read sequences. In brief, it will:

• Trim low quality reads and adapters, then consolidate duplicates.
• Map retained reads against a custom reference database (provided in this repository).
• Use custom scripts to generate consensus sequences for each genome segment by re-mapping reads against the "best" (i.e. closest provided) reference sequences.
• Produce a MultiQC report with relevent metrics.

To use this pipeline:

• Ensure that samples are located in the same directory as these scripts, gzipped, and labeled as:
  • <isolate_name>_R1.fastq.gz and <isolate_name>_R2.fastq.gz
• Clone this repository into your working directory and ensure that the following dependencies are installed:
  • fastQC, multiQC, mosdepth, picard
  • bowtie2, trimmomatic, cd-Hit, samtools, bcftools
• Finally, initiate the pipeline by running the run_mapping_pipeline_one_sample script along with your <isolate name> as a command line argument.

Please make sure to update local paths to TRIMMOMATIC .jar files or this pipeline will not work.