jeff-k / ngs-sim

Synthetic next-generation sequencing data with artefacts

ngs-sim

Synthetic next-generation sequencing data with artefacts

Mixtures

Multiple fasta references and mutation profiles can be provided. A proportion argument specifies the concentration of each. If no proportion is specified the default is 1.

Mutations

Mutations are defined in an ad hoc "variant call format" file. This is a list of:

position	deletions	insertions

Where position is the 0 indexed position in the reference sequence, deletions is the number of bases to remove, and insertions is the string of bases to insert.

Simulating sequencing artefacts

Optionally, the sequencing error profile is defined as a transition matrix.

Simulation

The simulation chains the following passes:

• mutation: specified variants are spiked into the reference
• amplification: the sequencing error profile is applied
• fragmentation: mutated strands are truncated to the mean and std fragment size. Pairs of mated reads are read from the ends. The second mate is reverse complemented.