The quality analysis pipeline PIQA was developed by the authors to be used in conjunction with Genome Analyzer software to examine genomic reads. It allows the user to more easily identify technical problems using both statistical and visual information.

This paper used whole transcriptome shotgun sequencing, using the Genome Analyzer II system, to investigate follicular lymphoma transcriptome. They assembled the equivalent of around 1% of the genome using ABySS. Transcriptome assembly needs to take into account factors such as gene expression levels, isoforms, and gene families. It is useful for, among other things, finding alternative splicing events, novel transcripts, and expression levels of various transcriptome properties. They used ABySS-Explorer for assembly visualization, which can incorporate long insert paired-end sequencing data.

Piwi-interacting RNAs (piRNAs) are transposon silencers that act as guides for a subfamily of Argonaute proteins—PIWI proteins—expressed in germline cells. The authors used flies with ago3 loss-of-function mutations to show that Ago3 increases levels of these piRNAs. The also show a separate, simpler, somatic, piRNA pathway that does not rely on Ago3 amplification. They used the Genome Analyzer for small RNA sequencing.

The authors developed immuno-SSAKE (iSSAKE) assembly software to investigate T-cell metagenomes utilizing the unique profile of the CDR3. They paired the alignment of sequenced short reads, constructed using the Genome Analyzer, and seeded de novo assembly. They created 20 million reads (36, 42, or 50 nt) with 1-2% random error, and seeded “iSSAKE de novo assemblies of CDR3.” The use of 42 nt and 50 nt reads to characterize sTCRß sequences was more sensitive than 36 nt reads.