raw2consensus

This container generates consensus sequences of M. tuberculosis raw reads in a list of target regions. It requires the reads, a CSV file with coordinates of the target regions, and a name for the output FASTA file. bwa-mem2 is used for aligning the reads against H37Rv (asm19595v2) and variants are called with freebayes. The CSV file with the target regions should have the header line 'locus,start,end'.

Usage

FASTQ files with forward and reverse M tuberculosis reads and a CSV file specifying the target loci are required as input. The container uses /data as working directory and will create the output file there.

docker run -v $PWD:/data \
    julibeg/tb-ml-consensus-seqs-from-raw-reads:v0.1.1 \
    -r target_loci.csv \
    -o consensus_seqs.fasta \
    my-sample_1.fastq.gz \
    my-sample_2.fastq.gz