SOAP (short oligonucleotide alignment program) can be used to align massive amounts of short reads to a reference genome. The authors developed SOAP2, which indexes the reference sequence in the main memory using the Burrows Wheeler Transformation (BWT) compressed index and is designed for improved Illumina Genome Analyzer sequencing. They used paired end reads and found SOAP2 gives 20 times improved alignment speed and uses almost two-thirds less memory. It is compatible for read lengths up to 1024 bp.

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.

Amplification artifacts can cause duplicated sequences which can weight read coverage and effect genome assembly and variation analysis. To counter this, the authors utilized (G+C) poor, neutral, or rich genomes from Plasmodium falciparum, Escherichia coli, and Bordetella pertussis, respectively. They developed a library preparation method without PCR but with fully ligated template strands being enriched by the cluster amplification step of the Genome Analyzer II system. This improved SNP detection, especially for P. falciparum, simplified assembly, and speeded up experimentation time.

To investigate gene-expression in a colon cancer cell line, the authors used their own “oligo-capping method” and the Genome Analyzer to conduct a massively parallel sequencing study. They examined positional information of transcriptional start sites (TSSs) and gene expression with a comparison between cells in both normal and hypoxic conditions. They found genome-wide transcriptional alterations between the two conditions, including regions with enriched hypoxia-induced promoters. Their methods enabled “absolute quantification of the transcripts” without the need for probes or PCR primers.