The Gigsaw NextGen Sequence Assembly Simulator

Gigsaw is a script that produces a physical model simulation of Next Generation Sequencing experiments. These models are ideal for teaching and illustrating the concepts and challenges of Next Generation Sequencing. The model is created as PDF which can then be printed and cut out. You can run Gigsaw here or there are some pre-prepared examples below. More experiment examples are welcome.

Easy de novo assembly

No Errors, No repeats. Just attempt to assemble the reads into one contig. Take note of the coverage (number of reads aligned) at each position to see that it is even. The reference sequence can be used to check your assembly.

Hard de novo assembly

Some errors, some repeats. It is not possible to reliably build just one correct contig from the single end data. This can potentially be solved by adding in paired end data. Check your assembly against the reference sequence

Mutation detection

Aligning the reads against the reference sequence highlights two variations. If you translate from the first ATG then one of the variants is silent, the other results in an amino acid change.

SNP detection

There are two SNPs and plenty of errors observed when you align the reads against the reference sequence

RNAseq exon analysis

Only the reads from the mRNA which are almost entirely within an exon will align against the genome sequence. The other reads will bridge between the two obvious exons.