Aaryan Lokwani
A Bioinformatician
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SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2285 days ago
https://bitbucket.org/genomeinformatics/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.
- The 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 length
- Quality values and number of passes depend on fragment length.
- Provided subread error probabilities are modified according to number of passes
- Outputs reads in FASTQ format and alignments in SAM format
