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Reference aligner indexes. Next-generation sequencing aligners require the reference sequence to be indexed prior to alignment, as this greatly increases alignment speed. An index consists of a set of files (Figure 1) and are generally aligner specific. For example, if you wish to align using BWA, you need a BWA index.
Figure 1. BWA reference aligner index files for human hg18 assembly
Some of the supported aligners share indexes. If you want to align using Tophat, the Bowtie aligner indexes can be used. If you want to align using Tophat2, the Bowtie2 aligner indexes can be used.
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Annotation models are used for quantification in gene expression analyses, annotating detected variants (e.g. to predict amino acid changes), visualizations in Chromosome view, generating coverage reports and for aligner index creation (see Adding Aligner Indexes Based on an Annotation Model). Typical file formats include GTF, GFF, GFF3 and BED.
Figure 2. Annotation models are displayed in separate tables.
The gray arrows (/
) next to the annotation model name expand/collapse each table. The three annotation models displayed in Figure 2 are different versions from the same source (RefSeq), distinguishable by their date. Aligner indexes (e.g. for alignment to the transcriptome) are added to the table of the corresponding annotation model.
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