The pipeline can assemble a (near) complete plastome genome from short reads automatically. It firstly carries out denovo assembly and then reference-based assembly if denovo fails to achieve a complete and quality contig. It is useful for large-scale chloroplast genome sequencing projects. For a single or few samples, please try NOVOPlasty, GetOrganelle or others.
Usage:
perl auto_assembly.pl [options] <samples_list> <reads_path>
Example:
perl auto_assembly.pl -outdir output -step abcdefghijk samples_list /home/xzhong/working_data_01/01_Assembly
########## description ##########
step a: remove adapter sequences using cutadapt.sh;
step b: normalize read depth based on kmer counts using bbnorm.sh;
step c: correct read errors using spades.sh;
step d: merge paired-end reads into single reads by overlap detection using flash.sh or bbmerge.sh[default];
step e: assemble using Velvet;
setp f: link assembled contigs to be a single long contig using Chloe2.jar or *.pl;
step g: fill gaps using Gapfiller;
step h: map reads back to the single contig using BWA;
step i: check, improve and report the assembly quality using Pilon;
step j: statistics;
step k: remove temporary files.
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The workflow is lack of maintenance nowadays...