Table 1 Taxonomic metagenome profiling pipelines used by participants in the challenge
Team | Preprocessing | QC | Filtering | Classification | Quantification |
|---|---|---|---|---|---|
1 | NA | FastQC (version not specified) | NA | Kraken v1.0 against bacteria | Bracken (version used for the challenge, commited code: March 5, 2018) |
2 | NA | FastQC (version not specified) | FastQC | Kraken v1.0 using bacterial database | Kraken v1.0 |
3 | NA | FastQC (version not specified) | FastQC | Kraken v1.0 against full database | Kraken v1.0 |
4 | Removal of host contamination by BWA v0.7.12 mapping on mouse genome | BWA v0.7.12 mapping against complete NCBI bacterial genomes | SAMtools v1.8 filtering in to keep bacterial reads only | BWA v0.7.12 mapping against complete NCBI bacterial genomes | Kaiju v1.6.2 |
5 | NA | BWA v0.7.12 mapping against RefSeq bacterial genomes | SAMtools v1.8 filtering in to keep bacterial reads only | BWA v0.7.12 mapping against RefSeq bacterial genomes | Kaiju v1.6.2 |
6 | PEAR v0.9.10 for merging of overlapping read pairs | FastQC v0.11.7 | NA | CLARK v1.2.5 using NCBI/RefSeq bacterial and archaeal genomes as reference (13.06.2018) | CLARK v1.2.5 |
7 | NA | FastQC (version not specified) | NA | Kaiju v1.6.2 using NCBI/RefSeq bacterial and archaeal genomes as reference | Kaiju v1.6.2 |
8 | Selection of 16S rRNA reads by BLASTN (version not specified) in clustered RDP database and concatenation of read pairs | SeqTools (version not specified) | NA | BLASTN (version not specified) against concatenated read pairs (using RDP as reference database) followed by taxon determination using TargetMine custom script | Sequence counts divided by 16S copy number |