Open Access Highly Accessed Research article

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

Barbara Feldmeyer1*, Christopher W Wheat2, Nicolas Krezdorn3, Björn Rotter3 and Markus Pfenninger1

Author Affiliations

1 Biodiversity and Climate Research Center (BiK-F), Molecular Ecology Group, Biocampus Siesmayerstraße, Goethe-Universität, 60323 Frankfurt am Main, Germany

2 Department of Biological and Environmental Sciences, Viikinakaari 1, FI-00014 University of Helsinki, Finland

3 GenXPro, Altenhöferallee 3, Frankfurt am Main, Germany

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BMC Genomics 2011, 12:317  doi:10.1186/1471-2164-12-317

Published: 16 June 2011

Additional files

Additional file 1:

Net coverage bp of R. balthica mitochondrial genes. Coverage bp of R. balthica mitochondrial genes by contigs > 80% bp identity. Numbers in parentheses indicate the number of contigs with identities > 80% matching the respective gene, and thus are included in the net coverage calculation. Combined coverage: overall coverage, thus bp identity of all first assembly contigs taken together.

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Additional file 2:

Gene ontology distribution of R. balthica contigs. Pie charts showing the distribution of contigs > 200bp, giving identical BLASTX gene hits for the NGEN and OASESkmer-31 assemblies, into the three main gene ontology categories.

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Additional file 3:

Microsatellite repeat motifs obtained from NGEN contigs. List with NGEN contigs containing di-, tri-, tetra-, penta-repeat motives with a minimum repeat length of six, contig ID, repeat type, size, position and contig sequence.

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Additional file 4:

Screen shot contig assembly vs. mitochondrial genome. The effect of a subsequent meta-assembly on contig redundancy is depicted here: a) Coverage of the mitochondrial gene COIII after the first separate assemblies and b) after the meta-assembly.

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Additional file 5:

Rearing conditions subjected to Radix balthica individuals.

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Additional file 6:

RNA quality inspection. RNA quality, RNA normalization, and RNA size selection gel pictures.

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Additional file 7:

VELVET assembly contigs.

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Additional file 8:

OASESkmer-21 assembly contigs.

Format: FAS Size: 14.2MB Download file

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Additional file 9:

OASESkmer-31 assembly contigs.

Format: FAS Size: 13MB Download file

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Additional file 10:

NGEN assembly contigs.

Format: FAS Size: 19MB Download file

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Additional file 11:

Meta-assembly contigs.

Format: ZIP Size: 6.9MB Download file

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