Additional file 1: of MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data

Supplementary figures, notes, and tables. (PDF 3297 kb

Subtelomeric repeats occupy the same nucleus territory as TgChromo1.

<p>FISH/IFA of TgChromo1-HA (green) and chromosome IX telomeric repeats (red). Parasite nuclei are labelled with DAPI (blue). Colocalising signals from FISH and IFA are arrowed.</p

Comparison of F-measures between the 200(V3) and 400(V4-V5) amplicon at the family level (left) and at the genus level (right) on the HC 50k dataset with error simulation.

<p>Comparison of F-measures between the 200(V3) and 400(V4-V5) amplicon at the family level (left) and at the genus level (right) on the HC 50k dataset with error simulation.</p

TgChromo1 binds to peri-centromeric heterochromatin.

<p>ChIP on chip was performed with the TgChromo1 antibody (anti-CHD1, red) or the anti-HA antibody (HA, black) and hybridized on a genome-wide tiling microarray. The regions of enrichment for H3K9me3 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032671#pone.0032671-Brooks1" target="_blank">[12]</a> are represented in blue. A snapshot of the 12 chromosomes where a centromere was identified <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032671#pone.0032671-Brooks1" target="_blank">[12]</a> is presented. ChIP on chip signals are represented as a log2 ratio of the signal given by the immunoprecipitated DNA over the input and plotted according to the genomic position of the oligonucleotide.</p

Histogram of wall time (colored) and CPU time (white), and peak memory usage (red crosses) for each standalone pipeline on three different datasets.

<p>Histogram of wall time (colored) and CPU time (white), and peak memory usage (red crosses) for each standalone pipeline on three different datasets.</p

F-measure and richness index error percentage after taxonomic merging for each pipeline on the 200(V3) 50k HC dataset with error simulation, when using different databases (the recommended database for each pipeline is marked with *).

<p>F-measure and richness index error percentage after taxonomic merging for each pipeline on the 200(V3) 50k HC dataset with error simulation, when using different databases (the recommended database for each pipeline is marked with *).</p

Comparison of F-measures (top) and richness error (bottom) in the error-free and error-prone sequencing models on the 200(V3) HC 50k dataset.

<p>Comparison of F-measures (top) and richness error (bottom) in the error-free and error-prone sequencing models on the 200(V3) HC 50k dataset.</p

TgChromo1 is maintained near the centrosome and the centrocone throughout the cell cycle.

<p><b>A:</b> IFA of TgChromo1-HA (green) and centrin1 (red), a marker of the centrosome. Parasite nuclei are labelled with DAPI (blue) at the interphase (G1), mitosis and the beginning of budding. <b>B:</b> IFA of TgChromo1-HA (green) and MORN1 (red), a marker of the centrocone. Parasite nuclei are labelled with DAPI (blue) at the interphase (G1), mitosis and the beginning of budding.</p

Chao1 values before taxonomic merging for clustering-first pipelines, and at the family level after taxonomic merging for all pipelines, at three different complexities, on the 50k 200(V3) with error simulation datasets.

<p>LC, MC and HC were all composed of 50 bacterial families, in varying proportions.</p

Comparison of the richness (Chao1) and diversity (Inverse Simpson) indexes for clustering-first pipelines before taxonomic merging, on the 200(V3) HC dataset with sequencing errors simulation when generating 25k, 50k and 100k sequences.

<p>Comparison of the richness (Chao1) and diversity (Inverse Simpson) indexes for clustering-first pipelines before taxonomic merging, on the 200(V3) HC dataset with sequencing errors simulation when generating 25k, 50k and 100k sequences.</p