Package: simlord
SimLoRD is a read simulator for third generation sequencing reads and is
currently focused on the Pacific Biosciences SMRT error model.Reads are simulated from both strands of a provided or randomly
generated reference sequence.FeaturesThe reference can be read from a FASTA file or randomly generated
with a given GC content. It can consist of several chromosomes, whose
structure is respected when drawing reads. (Simulation of genome
rearrangements may be incorporated at a later stage.)The read lengths can be determined in four ways: drawing from a
log-normal distribution (typical for genomic DNA), sampling from an
existing FASTQ file (typical for RNA), sampling from a a text file
with integers (RNA), or using a fixed lengthQuality values and number of passes depend on fragment length.Provided subread error probabilities are modified according to number
of passesOutputs reads in FASTQ format and alignments in SAM formatSystem requirementspython3scipynumpypysamdinopyWe recommend usingminicondaand
creating an environment for SimLoRD# Create and activate a new environment called simlord
conda create -n simlord python=3 pip numpy scipy cython
source activate simlord

# Install packages that are not available with conda from pip
pip install pysam
pip install dinopy
pip install simlord

# You now have a 'simlord' script; try it:
simlord --help

# In case of a new version update as follows:
pip install simlord --upgrade

# To switch back to your normal environment, use
source deactivatePlatform supportSimLoRD is a pure Python program. This means that it runs on any
operating system (OS) for which Python 3 and the other packages are
available.Example usageExample 1:Simulate 10000 reads for the reference ref.fasta, use the
default options for simulation and store the reads inmyreads.fastqand the alignment inmyreads.sam.simlord  --read-reference ref.fasta -n 10000  myreadsExample 2:Generate a reference with 10 mio bases GC content 0.6
(i.e., probability 0.3 for both C and G; thus 0.2 probability for both A
and T), store the reference as random.fasta, and simulate 10000 reads
with default options, store reads asmyreads.fastq, do not store
alignments.simlord --generate-reference 0.6 10000000 --save-reference random.fasta\
        -n 10000 --no-sam  myreadsExample 3:Simulate reads from the givenreference.fasta, using
a fixed read length of 5000 and custom subread error probabilities (12%
insertion, 12% deletion, 2% substitution). As before, save reads asmyreads.fastqandmyreads.sam.simlord --read-reference reference.fasta  -n 10000 -fl 5000\
        -pi 0.12 -pd 0.12 -ps 0.02  myreadsA full list of parameters, as well as their documentation, can be foundhere.Last ChangesVersion 1.0.4 (2020-01-07)Bugs fixedAdded missing else for parameter sam_output.Other ChangesChanged read names.New read name format: ‘m{read_number}/{read_length}/CCS read_information’Added parameter –old-read-names for old read names where all information is encoded in one large string delimited by ‘;’.Version 1.0.3 (2019-05-20)New FeaturesAdded new parameter –gzip to gzip the output reads fastq file.If “-” instead of a filename is given, the reads are printed to sdt-out.In this case without further specification the sam-file gets the name “reads.sam” in the current working directory.Other ChangesChanged coverage parameter from int to float allowing fractional coverage values.Changed delimiter in read id from _ to ;Added chromosome name to read idChanged id of mate read in sam file to result in “*” instead of “=”.Changed fastq writing from text to byte writing to speed up I/OVersion 1.0.2 (2017-03-17)New FeaturesDraw chromosomes for reads weighted with their length instead of equal distributed. This leads to a equal distributed read coverage over the chromosomes. Previous behaviour with equal probabilities for each chromosome can be activated with parameter –uniform-chromosome-probability.Parameter –coverage: Determine number of reads depending on the desired read coverage of the whole reference genome.Parameter –without-ns: Sample the reads only from regions completly without Ns.Warning: Using –without-ns may lead to biased read coverage depending on the size of contigs without Ns and the expected readlength.Bugs fixedCIGAR string had sometimes wrong count of last match because of false extension after deletion.Version 1.0.1 (2017-01-03)Bugs fixedRemoved nargs=1 at parameter –probability-threshold leading to an error when changing the parameter.Version 1.0.0 (2016-07-13)API ChangesChanged SEQ in SAM file to reverse complemented read instead of the original read for reads mapping to the reverse complement of the reference.Example:reference       ATCG     read   CAAT
true alignment  ||X|
                ATTG

Before: SEQ CAAT and CIGAR string 2=1X1=
Now:    SEQ ATTG and CIGAR string 2=1X1=LicenseSimLoRD is Open Source and licensed under theMIT
License.