Track | Process | Tool | Input | Output |
---|---|---|---|---|
CloVR-Search | Database search | BLAST [60] | nt or pep FASTA | BLAST output |
CloVR-Microbe[38] | Assembly | Raw sequence data (SFF, nt.FASTA1, nt.FASTQ1) | nt.FASTA | |
 | Gene prediction | Glimmer3 [62] |  | pep.FASTA |
 | tRNA prediction | tRNA-scan [63] |  | GBK, SQN |
 | rRNA prediction | RNAmmer [64] |  | GBK, SQN |
 | Functional annotation | BLASTX against UniRef100 [58] and COG [65], HMMER [66] search against Pfam [67] and TIGRfam [68] |  | Annotated GBK, SQN |
CloVR-16S [39] | Quality checking | nt.FASTA | nt.FASTA | |
 | Taxonomic classification | RDP classifier [69] |  | raw output, summary reports |
 | Multiple sequence alignment | Mothur, Qiime (PyNAST) |  | nt.FASTA alignments |
 | OTU clustering | Mothur (distance matrix), Qiime (uclust [70]) |  | OTU list/table |
 | α-diversity analysis | Mothur (collectors curves, rarefaction curves, diversity and richness estimators) |  | summary reports/diversity curves |
 | β-diversity analysis | Metastats [71], custom R scripts, Qiime |  | summary reports/figures |
CloVR-Metagenomics[40] | Clustering and artificial replicate removal | UCLUST | nt.FASTA | nt.FASTA |
 | Functional classification | BLASTX against COG |  | raw output, summary reports |
 | Taxonomic classification | BLASTN against RefSeq [72] |  | raw output, summary reports |
 | Comparative analysis | Metastats, custom R scripts |  | summary reports/figures |