Table 1.
VEBA modules
| Module | Description | Docker Registry |
|---|---|---|
| preprocess | Fastq quality trimming, adapter removal, decontamination, and read statistics calculations (short reads) | https://hub.docker.com/r/jolespin/veba_preprocess |
| preproces-long | Fastq quality trimming, adapter removal, decontamination, and read statistics calculations (long reads) | https://hub.docker.com/r/jolespin/veba_preprocess |
| assembly | Assemble reads, align reads to assembly, and count mapped reads (short reads) | https://hub.docker.com/r/jolespin/veba_assembly |
| assembly-long | Assemble reads, align reads to assembly, and count mapped reads (long reads) | https://hub.docker.com/r/jolespin/veba_assembly |
| coverage | Align reads to (concatenated) reference and counts mapped reads (short reads) | https://hub.docker.com/r/jolespin/veba_assembly |
| coverage-long | Align reads to (concatenated) reference and counts mapped reads (long reads) | https://hub.docker.com/r/jolespin/veba_assembly |
| binning-prokaryotic | Iterative consensus binning for recovering prokaryotic genomes with lineage-specific quality assessment | https://hub.docker.com/r/jolespin/veba_binning-prokaryotic |
| binning-eukaryotic | Binning for recovering eukaryotic genomes with exon-aware gene modeling and lineage-specific quality assessment | https://hub.docker.com/r/jolespin/veba_binning-eukaryotic |
| binning-viral | Detection of viral genomes and quality assessment | https://hub.docker.com/r/jolespin/veba_binning-viral |
| classify-prokaryotic | Taxonomic classification of prokaryotic genomes | https://hub.docker.com/r/jolespin/veba_classify-prokaryotic |
| classify-eukaryotic | Taxonomic classification of eukaryotic genomes | https://hub.docker.com/r/jolespin/veba_classify-eukaryotic |
| classify-viral | Taxonomic classification of viral genomes | https://hub.docker.com/r/jolespin/veba_classify-viral |
| cluster | Species-level clustering of genomes and lineage-specific orthogroup detection | https://hub.docker.com/r/jolespin/veba_cluster |
| annotate | Annotates translated gene calls several databases | https://hub.docker.com/r/jolespin/veba_annotate |
| phylogeny | Constructs phylogenetic trees given a marker set | https://hub.docker.com/r/jolespin/veba_phylogeny |
| index | Builds local or global index for alignment to genomes | https://hub.docker.com/r/jolespin/veba_mapping |
| mapping | Aligns reads to local or global index of genomes | https://hub.docker.com/r/jolespin/veba_mapping |
| biosynthetic | Identify biosynthetic gene clusters in prokaryotes and fungi | https://hub.docker.com/r/jolespin/veba_biosynthetic |
| profile-pathway | Pathway profiling of de novo genomes | https://hub.docker.com/r/jolespin/veba_profile |
| profile-taxonomy | Taxonomic profiling of de novo genomes | https://hub.docker.com/r/jolespin/veba_profile |