✅
usage: iRep [-h] -f [F [F ...]] -s [S [S ...]] -o O [--pickle] [-mm MM] [-c C]
[--sort] [-M M] [--no-plot] [--no-gc-correction] [-ff] [-t T]
# calculate the Index of Replication (iRep)
optional arguments:
-h, --help show this help message and exit
-f [F [F ...]] fasta(s)
-s [S [S ...]] sorted sam file(s) for each sample (e.g.: bowtie2
--reorder)
-o O prefix for output files (table and plots)
--pickle save pickle file (optional)
-mm MM max. # of read mismatches allowed (default: 1)
-c C window coverage threshold (default = 8 x median)
--sort optional - sort the sam file
-M M max. memory (GB) for sorting sam (default: 100)
--no-plot do not plot output
--no-gc-correction do not correct coverage for GC bias before calculating
iRep
-ff overwrite files
-t T threads (default: 6)usage: bPTR [-h] [-f [F [F ...]]] [-s [S [S ...]]] -m M [-c C] -o O
[-pickle PICKLE] -plot PLOT [-mm MM] [-p P] [--sort] [-b B] [-ff]
[-t T]
# est. growth rate from peak-to-trough coverage ratio
optional arguments:
-h, --help show this help message and exit
-f [F [F ...]] fasta(s)
-s [S [S ...]] sorted sam file(s) for each sample (e.g.: bowtie2 --reorder)
-m M method for detecting Ori/Ter of replication: gc_skew or
coverage
-c C pre-computed data from growth_ptr.py (optional: pickle file)
-o O filename for output table
-pickle PICKLE filename for output pickle file (optional)
-plot PLOT filename for coverage profile plots (default: no plots)
-mm MM maximum number of mapping mismatches allowed (default: no
limit)
-p P number of permutations to perform (default: None)
--sort sort the sam file
-b B max memory (GB) for sorting sam (default: 100)
-ff overwrite files
-t T threads (default: 6)