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Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggestedthat in a string graph or equivalently a unitig graph, any path spells a validassembly. As a string/unitig graph also encodes every valid assembly of reads,such a graph, provided that it can be constructed correctly, is in fact alossless representation of reads. In principle, every analysis based onwhole-genome shotgun sequencing (WGS) data, such as SNP and insertion/deletion(INDEL) calling, can also be achieved with unitigs.  Results: To explore the feasibility of using de novo assembly in the contextof resequencing, we developed a de novo assembler, fermi, that assemblesIllumina short reads into unitigs while preserving most of information of theinput reads. SNPs and INDELs can be called by mapping the unitigs against areference genome. By applying the method on 35-fold human resequencing data, weshowed that in comparison to the standard pipeline, our approach yields similaraccuracy for SNP calling and better results for INDEL calling. It has highersensitivity than other de novo assembly based methods for variant calling. Ourwork suggests that variant calling with de novo assembly be a beneficialcomplement to the standard variant calling pipeline for whole-genomeresequencing. In the methodological aspects, we proposed FMD-index forforward-backward extension of DNA sequences, a fast algorithm for finding allsuper-maximal exact matches and one-pass construction of unitigs from anFMD-index.  Availability: http://github.com/lh3/fermi  Contact: hengli@broadinstitute.org

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly