SIMulator for Long read transcriptome Analysis with RNA DecaY model
git clone https://github.com/shinichinamba/simlady.git
cd simlady
pip3 install .simlady --helpusage: simlady [-h] [--version] [--fold-changes PATH] [--num-reads INT]
[--num-reps [INT [INT ...]]] [--gtf PATH]
[--gamma-params PAR PAR] [--chi2-params-s PAR PAR PAR PAR PAR]
[--chi2-params-n PAR PAR PAR] [--max-passes INT]
[--sqrt-params PAR PAR] [--norm-params PAR PAR]
[--probability-threshold FLOAT] [--prob-ins FLOAT]
[--prob-del FLOAT] [--prob-sub FLOAT] [--min-readlength INT]
[--lognorm-readlength [PARAMETER [PARAMETER ...]] |
--sample-readlength-from-fastq PATH [PATH ...] |
--sample-readlength-from-text PATH | --asis-fold-changes]
[--sam-output SAM_OUTPUT] [--no-sam]
[--transcriptomic-fasta-output PATH] [--write-weights]
[--threads INT] [--save-memory] [--seed INT] [--gzip] [--bam]
FASTA_PATH OUTPUT_PREFIX
simlady v0.1.0 -- simlady: a SIMulator for Long read transcriptome Analysis
with RNA DecaY model. Simlady uses the Pacific Biosciences SMRT error model
which is implemented in SimLoRD.
positional arguments:
FASTA_PATH A transcriptomic fasta file to sample reads from, or a
genomic fasta file if you specify '--gtf' flag.
gzipped file is allowed.
OUTPUT_PREFIX Save the simulated reads as a fastq-file at
OUTPUT_PREFIX.fastq
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--fold-changes PATH, -fc PATH
Read fold changes from PATH. Each line must have the
same number with tab-delimited format and be arranged
in the same row order as a reference transcript fasta,
empty for no fold change.
--num-reads INT, -n INT
Number of reads to simulate (default= 1000).
--num-reps [INT [INT ...]], -r [INT [INT ...]]
Number of repeats par groups. If you specify '--fold-
changes' option, number of groups must be same as the
column number of fold-changes file. Otherwise 1
(default= [1]).
--gtf PATH, -g PATH A transcriptomic gtf file with exonic features.
Transcriptomic sequences will be extracted from this
file and the genomic fasta file.
--gamma-params PAR PAR, -ga PAR PAR
Curve determining parameters for the gamma
distribution: shape and scale. (default= (0.07611007,
771.80272892))
--chi2-params-s PAR PAR PAR PAR PAR, -xs PAR PAR PAR PAR PAR
Parameters for the curve determining the parameter
scale for the chi^2 distribution: m,b, z, c, a for
'm*x + b' if x <= z and 'c * x^-a' if x > z (default=
(0.01214, -5.12, 675, 48303.0732881,
1.4691051212330266))
--chi2-params-n PAR PAR PAR, -xn PAR PAR PAR
Parameters for the function determining the parameter
n for the chi^2 distribution: m, b, z for 'm*x + b' if
x < z and 'm*z + b' for x >=z (default=
(0.00189237136, 2.5394497, 5500)).
--max-passes INT, -mp INT
Maximal number of passes for one molecule (default=
40).
--sqrt-params PAR PAR, -sq PAR PAR
Parameters for the square root function for the
quality increase: a, b for 'sqrt(x+a) - b' (default=
(0.5, 0.2247))
--norm-params PAR PAR, -nd PAR PAR
Parameters for normal distributed noise added to
quality increase sqare root function (default= (0,
0.2))
--probability-threshold FLOAT, -t FLOAT
Upper bound for the modified total error probability
(default= 0.2)
--prob-ins FLOAT, -pi FLOAT
Probability for insertions for reads with one pass.
(default= 0.11)
--prob-del FLOAT, -pd FLOAT
Probability for deletions for reads with one pass.
(default= 0.04)
--prob-sub FLOAT, -ps FLOAT
Probability for substitutions for reads with one pass.
(default= 0.01)
--min-readlength INT, -mr INT
Minimum read length (default= 50) for lognormal
distribution
--lognorm-readlength [PARAMETER [PARAMETER ...]], -ln [PARAMETER [PARAMETER ...]]
Parameters for lognormal read length distribution:
(sigma, loc, scale), empty for defaults. (default =
(0.200110276521, -10075.4363813, 17922.611306))
--sample-readlength-from-fastq PATH [PATH ...], -sf PATH [PATH ...]
Sample read length from a fastq-file at PATH
containing reads.
--sample-readlength-from-text PATH, -st PATH
Sample read length from a text file (one length per
line).
--asis-fold-changes, -af
Do not consider read length but use fold change as is.
--sam-output SAM_OUTPUT, -so SAM_OUTPUT
Save the alignments in a transcript sam-file at
SAM_OUTPUT. By default, use OUTPUT_PREFIX.sam. If '--
bam' option is specified, use OUTPUT_PREFIX.bam
--no-sam Do not calculate the alignment and write a sam file.
--transcriptomic-fasta-output PATH, -to PATH
A path to save a transcriptomic fasta file. By
default, use OUTPUT_PREFIX.tx.fasta. This option is
ignored unless you specify --gtf option.
--write-weights Write out the weights matrix as a tab-delimited file.
The file name will be OUTPUT_PREFIX.weights.txt.
--threads INT, -T INT
Number of threads. Increasing the number of threads
makes the processing faster at the expense of larger
memory requirement (default= 1)
--save-memory For saving memory, provoke multiprocessing only for
calculating weight matrix and not for generating
reads.
--seed INT Specify a seed of random generators. You should also
match number of threads for reproducibility.
--gzip Compress the simulated reads using gzip and save them
at OUTPUT_PREFIX.fastq.gz
--bam Save the simulated sam files in BAM format.
Simlady uses the Pacific Biosciences SMRT error model which is implemented in SimLoRD.
S Namba et al. Multi-sample Full-length Transcriptome Analysis of 22 Breast Cancer Clinical Specimens with Long-Read Sequencing. BioRxiv (2020) https://doi.org/10.1101/2020.07.15.199851