This a working repository for development of a Python wrapper script to automate assembly of mtDNA genomes from off target reads in hybridization capture experiments. Currently, it also includes a shell script for the same purpose.
Script: mtDNA_assembler.sh
Description: This script should search for mtDNA reads, create a seed file, and start a PRICE assembly of mtDNA genomes
Requires: blatq; excerptByIDs (The Go programming language must be installed to run this); Price; SPAdes
Authorship: Originally Jack Dumbacher; modified and annotated by Ethan Linck
To begin, you'll need...
- A reference mtDNA genome of your organism or a close relative (here
t_sanctus.fasta)... - Forward (
EL_hyRAD_001A_S29_1), reverse (EL_hyRAD_001A_S29_2), and unpaired (EL_hyRAD_001A_S29_u) reads from a single sample... - All required programs installed and working
- An edited version of mtDNA_assembler.sh with correct sample IDs and paths for your own system, and correct parameters for the PRICE assembler (see documentation here).
Then, simply execute the script:
$ bash mtDNA_assembler.sh
The script will proceed through four steps:
- blatq will search for reads that align with your reference mtDNA genome and create a list of matching
.fastqIDs; - excerptByIDs will take this list, extract matching sequences, and collate them into seeds;
- SPAdes will run an initial assembly on these seeds to increase downstream efficiency;
- The PRICE assembler will iteratively map reads to the edge of seeds and then contigs, merging identical sequences.
Ultimately, this should output a .fasta for each cycle, with the terminal cycle representing the most complete assembly (e.g., EL_hyRAD_001A_mtDNA.cycle30.fa).
Script: mtDNA_assembler.py
Description: A work in progress...