WARNING : WORKFLOW IS STILL UNDER DEVELOPMENT AND MAY NOT FUNCTION AS ADVERTIZED IN THIS README

Introduction

emcal23/VectorDetective is a bioinformatics pipeline that takes PCR-amplified mosquito and bloodmeal NGS library preps to a searchable consensus sequence.

1. Takes paired-end fastq files
2. Read QC (FastQC)
3. Aligns the reads to references of gene targets
4. Extracts reads/consensus from targets

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,fastq_1,fastq_2
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Now, you can run the pipeline using:

nextflow run emcal23/VectorDetective \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --blast_db <path/to/blast/database/> \ #optional
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

Consensus fasta or fastq's converted to fastas.

For more details about the output files and reports, please refer to the output documentation.

Credits

emcal23/VectorDetective was originally written by @emcal23 and @erinyoung.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.