This directory contains two scripts which can be used to interpet the output of uncalled sim.
We understand these scripts may not be the most user friendly. We will work towards improving them and better intergrate them with the simulator in the future.
Example:
> sim_scripts/est_genome_yield.py -u uncalled_out.paf --enrich -x E.coli -m mm2.paf -s sequencing_summary.txt --sim-speed 0.25
unc_on_bp 150.678033
unc_total_bp 6094.559395
cnt_on_bp 33.145022
cnt_total_bp 8271.651331
This is designed to be used in the context of enriching/depleting for whole genomes or chromosomes.
Arguments:
-u/--uncalled-fname: Simulator output PAF file-s/--seq_sum: Control sequencing summary-m/--minimap-fname: Minimap2 PAF file of the control reads aligned to a reference containing the target (or off-target, in the case of depletion) sequences-x/--bwa-prefix: BWA reference used during the simulation--deplete/--enrich: same as option used in simulation-t/--sim-speed: Speed that the simulator was run at in the range (0.0, 1.0]
Example:
> sim_scripts/est_bed_yield.py -u uncalled_out.paf -c ctl_coverage.bed -s sequencing_summary.txt -t 0.25
unc_on_bp 150.678033
unc_total_bp 6094.559395
cnt_on_bp 33.145022
cnt_total_bp 8271.651331
This is designed to be used when the targets are subsequences of a larger reference, for example a set of genes. This requires bedtools intersect -bed -a control_alns.bam -b targets.bed to be run prior, where control_alns.bam is minimap2 alignments of the basecalled control reads to the full reference, and targets.bed are the targeted regions.
Arguments:
-u/--uncalled-fname: Simulator output PAF file-c/--cov-fname: BED file of control read coverage. Should be output from 'bedools intersect' of control read alignments and the target region(s)-s/--seq-sum: Control sequencing summary- -t/--sim-speed: Speed that the simulator was run at