Effects of altering the -w parameter of SLP. The insertions and deletions are in units of events.

<p>Effects of altering the -w parameter of SLP. The insertions and deletions are in units of events.</p

Effects of altering the parameters of SeqNoise.

<p>A: The effects of altering the -c parameter in increments of 0.01, while keeping -s at the default of 30.0. B: The effects of altering -s in increments of 10, while keeping -c at the default of 0.08. C: The effects of altering -s in increments of 10, while keeping -c at the minimum of 0.01.</p

Effects of altering the percent_id parameter of denoiser.

<p>Effects of altering the percent_id parameter of denoiser.</p

Effects of aaltering the parmeters of PyroNoise.

<p>A: The effects of altering the -c parameter in increments of 0.01, while keeping -s at the default of 60.0. B: The effects of altering -s in increments of 10, while keeping -c at the default of 0.01.</p

Changes made to the reads at each step of the denoising pipelines.

<p>All data are in units of base pairs, except those indicated by * (units of events). Rank-abundance curves can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060458#pone.0060458.s025" target="_blank">Files S25</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060458#pone.0060458.s026" target="_blank">S26</a>.</p

The “accordion effect” of the Filtering and PyroNoise steps.

<p>A: The original reads’ lengths (Stage 0) were reduced by the Filtering step (Stage 1A). Note the increased number of reads in the 250 – 350 bp range. After clustering by PyroNoise (Stage 2A), the read lengths were increased again, similar to Stage 0. B: The numbers of changes at each position along the Stage 2A reads, when using either Stage 0 or Stage 1A as the reference.</p

The steps of three denoising pipelines.

<p>The reads were reconstituted at each stage following the steps, as described in the text. The reads will be referred to by their stage numbers throughout this paper.</p

Sequence information produced by the denoising pipelines.

<p>The lengths of the reads produced at the end of the three major denoising pipelines. The total sequence information is the area under the curve. The dotted lines represent the reads (post-Filtering) that were input to each of the pipelines. Both AmpliconNoise and the QIIME denoising pipeline expand this sequence information.</p

Assembled N50 contigs Ammodramus caudacutus

Fasta file of assembled contigs that were > the N50contig size of assembled Ammodramus caudacutus reads from Illumina sequencing

Assembled N50 contigs Ammodramus nelsoni

Fasta file of assembled contigs > than the N50 contig length for Illumina sequencing reads of Ammodramus nelsoni