Short DNA

MetaGenomeThreader

Statistic Section (short DNA Sequences)

After verifying the general functionality of the MetaGenomeThreader with long DNA sequences without sequencing errors and frame shifts, (cp. test data: long DNA sequences) it was tested with short DNA sequences including error settings for insertions and deletions that could lead to frame shifts and sequencing errors as shown in Tab. 2.2. The average sequence length was 120bp by a tenfold sequence coverage. The synthetic metagenome was constructed through the combination of the separate simulated DNA sequences (with the ReadSim simulator) of all three species. The synthetic metagenome is therefore abstracted from the diverse distribution of the organism numbers per species. Nevertheless the synthetic metagenome was good enough to prove the general functionality of the MetaGenomeThreader by the use of short DNA sequences.
species
(cp. Tab. 1.1) sequence length
(Ø) insertions deletions sequence coverage
(achieved) number of sequences
(high/low quality reads)
Candidatus Pelagibacter 120 359
(2,18%) 135
(0,82%) 10 (5,74) 251 (245/6)
Vibrio cholerae 120 339
(2,45%) 74
(0,53%) 10 (4,84) 251 (249/2)
Pyrococcus horikoshii 120 224
(2,13%) 62
(0,58%) 10 (5,48) 167 (164/3)
Tab. 2.2: Parameter settings for the simulation of the short DNA sequencing data

Based on the sequencing errors the original NCBI entries of the target species could appear under the statistic section. The statistic section of the metagenome analysis showed that there would be a high probability of a Pyrococcus and Vibrio species as part of the result. The same assumption would be made for Candidatus Pelagibacter as found in the long DNA sequences analysis (cp. test data: long DNA sequences).
target species
(cp. Tab. 1.1) number of species in the metagenome occurrence in the metagenome
(in % respectively level) 5 most dominant species for the PCS identification of the metagenome
Candidatus Pelagibacter 504 0,29% / 107 3,9141% Pyrococcus abyssi
3,7309% Pyrococcus furiosus
Vibrio cholerae 0,53% / 24 1,9172% Vibrio harveyi chromosome I
Pyrococcus horikoshii 0,84% / 12 1,9120% Vibrio vulnificus YJ016 chromosome I
1,9120% Vibrio vulnificus CMCP6 chromosome I
Tab. 2.3: MetaGenomeThreader statistic section summary of the metagenome analysis result (cp. statistic section summary by the use of long DNA sequences, here).
MetaGenomeThreader: Main

here

Test Results: Sequence Data

here

Test Results: Interpretation

here