Experiment1

Fasta files of amplicon reads from Experiment 1 for both the GS Junior and Ion Torrent. All fasta files are non-dereplicated and have been separated into sample batches based on MID (index) tags and all primers have been removed. No further quality or abundance filtering has been performed on the fasta file

Impact of analysis parameters on the numbers of taxonomic units obtained for a bulk-bone sample.

<p>A number of analysis parameters were used to analyse a complex mixture containing numerous taxa. Different quality and abundance filtering methods were used in addition to two taxonomy-independent measures of analysis, full definitions and explanations of which are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124671#pone.0124671.g001" target="_blank">Fig 1</a>. The spread in the numbers of taxonomic units obtained across the combinations of parameters chosen is seen. The radius of each semicircle represents the number of taxonomic units obtained given a set combination of the parameters used. The number of taxonomic units is also indicated above each semicircle. Each semicircle is proportional to all others. AFM—abundance filtering method; QFM—quality filtering method; TIM—taxonomy-independent method.</p

Average sequencing error rates across a single amplicon region.

<p>Average sequencing error rates are shown for multiple bird species across the whole of a short 12S rRNA gene region <b>(A)</b>. Additionally, the error profile across the gene region is shown for <i>Calyptorhynchus lathami</i> for both the Ion Torrent PGM <b>(B)</b> and MiSeq <b>(C)</b> with key. The error patterns observed were similar across all species sequenced. Error rates are shown across 5 bp segments and where error rates were above 1% for a single base this is indicated through the red circles.</p

Experiment5

Fasta file of amplicon reads from Experiment 5 for the Ion Torrent. The file non-dereplicated and has only been separated based on MID (index) tag. Primers have not been removed and no quality or abundance filtering has been performed on the fasta file

TCM_002

Plant Sequences from Traditional Chinese Medicine Sample No.

TCM_018

Plant Sequences from Traditional Chinese Medicine Sample No. 1

TCM_003

TCM_00

TCM_021

Animal and Plant Sequences from Traditional Chinese Medicine Sample No. 2

TCM_024

Animal Sequences from Traditional Chinese Medicine Sample No. 2

TCM_004

Plant Sequences from Traditional Chinese Medicine Sample No.