Read count benchmark at species level.

<p>Read count benchmark at species level.</p

PCR assembly validation.

<p>Contigs assembled from 93 bp single-end reads were validated using standard PCR. A: genomic DNA, B: First-strand cDNA synthesis with reverse transcriptase, C: First-strand cDNA synthesis without reverse transcriptase. M: 100 bp O’GeneRuler. For primer and contig sequences, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123887#pone.0123887.s001" target="_blank">S1 Table</a>.</p

Summary of qPCR-based estimates of haploid genome sizes.

<p>Summary of qPCR-based estimates of haploid genome sizes.</p

Benchmarking of the <i>in vitro</i> data mapped against a bacteria reference sequence database.

<p>Benchmarking of the <i>in vitro</i> data mapped against a bacteria reference sequence database.</p

Benchmarking of the <i>in silico</i> data mapped against a bacteria reference sequence database.

<p>Benchmarking of the <i>in silico</i> data mapped against a bacteria reference sequence database.</p

Summary of BLASTx search results of <i>D</i>. <i>muscipula</i> transcriptome.

<p>Summary of BLASTx search results of <i>D</i>. <i>muscipula</i> transcriptome.</p

Contig size distribution.

<p>Transcriptome assembly contig size distribution of all contigs (left) and predicted full-length contigs (right).</p

Genomic DNA purification and genome size estimate of <i>D</i>. <i>muscipula</i>.

<p><b>(A)</b> Agarose gel showing a purified fraction of <i>D</i>. <i>muscipula</i> genomic DNA (1) using a modified CTAB procedure. M1: DNA ladder D2000 (Tiangen), M2: DNA ladder λ-Hind3 digest (Takara). <b>(B)</b> Genome size estimate of <i>D</i>. <i>muscipula</i> using a single-copy qPCR method with <i>DmACT7</i> as amplicon. <i>A</i>. <i>thaliana</i> serves as a control, using <i>ACTIN1</i> as amplicon.</p

A schematic flowchart for processing of paired-end sequences with MGmapper.

<p>MGmapper processes fastq reads in four steps. These consist of: (I) Trimming and mapping reads against a phiX bacteriophage to remove potential positive control reads. (II) Mapping to specified reference databases, post-processing of BWA-mem alignments to remove reads with low alignment score or insufficient alignment coverage. (III) Identification of best hits in <i>bestmode</i>: Assignment of a read-pairs to only one specific reference sequence based on the highest sum of alignment scores. In <i>fullmode</i>, assigned a read-pair to a reference sequence even if a higher alignment score is found when mapping to another reference sequence database. This will provide best target match, considering only the sequences present in one particular reference database. (IV) Compilation of abundance statistics, read and nucleotide counts, depth, coverage, and summary reports.</p

Mock bacterial composition of <i>in vitro</i> and <i>in silico</i> datasets.

<p>Mock bacterial composition of <i>in vitro</i> and <i>in silico</i> datasets.</p