Configuration

1. Make sure you have the following dependencies installed:

   • Nextflow
   • Conda
   • AMBER (optional for authentication)

2. Create a Conda environment using the provided YAML file:

   conda env create -f container/env.yml
   

Running

The script called run:

  nextflow run com.nf \
        --fasta_info "61genus.info" \
        --reads "Steppe_bison.fastq.gz" \
        --fasta_index "~/extract_authentication/index/61genus" \
        --threads 10 \
        --label "61genus" \
        -with-trace

Input

--fasta_info: Specify the path to the fasta information file with the first column as the path to the fasta file and the second column as their name (reference ID), such as /path/to/A.fasta species_A /path/to/B.fasta species_B

--reads: Provide the reads to be mapped.

--fasta_index: Set the directory containing the bowtie2 index of the concatenated fasta file of all fasta files. It's /path/to/bowtie2_index without the suffix .bt2l

--threads: Number of threads to use (e.g., 10 in the example).

--label: Label used for output.

-with-trace: Reports time and memory usage.

Output

All outputs are stored in a directory results/

${label}_${reads_filename}.mapped_config_from has 5 columns: contig ID, reference ID, Contig length, the number of mapped read-segments, and the number of unmapped read-segments.

${label}_${reads_filename}_reads_sum.csv output 3 columns:

• species: reference ID

• n_reads_Sum: the number of reads mapped to this fasta file

• contigs_len_Sum: the total genome size summed from all contigs of the fasta file

Subdirectory of results/

• contigs: contigs ID corresponding to the reference ID given in .info file.

• mapping: bam and their index, also extracted bam file with only reads mapped to each fasta file, which has a -ext.bam as suffix.

• plot: damage plots for authentication