Results are written to <res-dir>/<sample>/ and logs to <logs-dir>/<sample>/. The results directory is set with -r (always pass it) and the sample name with -s; if -s is omitted, the sample name is derived from the input read filename.
For how to run the pipeline, see
| File or directory | Description |
|---|---|
| contigs/ | contigs sorted by taxa — one fasta per mapped order, family and genus |
| contigs.fa | all contigs in a single fasta file |
| contigs.ann1.{ab,ph,vi,un}.fa | archaeal+bacterial, bacteriophage, viral and unmapped contigs, from the 1st annotation round |
| contigs.ann2.{ab,ph,vi,un}.fa | the same, from the 2nd annotation round |
| contigs.orfs.aa.fa / contigs.orfs.nt.fa | predicted ORFs, as amino-acid and nucleotide sequences |
| scaffolds.fa | scaffolds, if available |
| abund_table.xlsx / .tsv | taxon abundancies |
| contig_annot.xlsx / contigs_annot.tsv | contig annotations |
| reports/krona.report.html | abundancies as an interactive Krona graph |
| reports/refgen.report.html | IGV reports: viral contigs aligned against reference genomes |
| taxprofile.txt | taxonomic profile in CAMI format |
| figures/ | contig and read length histograms |
| History.log | log of the command lines that produced this directory |
Table 1: LazypipeX output
Abundancies are segregated into separate tables by toptaxrank, and within each table displayed at three taxonomic levels: species, genus and family. Since NCBI's
| Column | Description |
|---|---|
| readn | read pairs assigned to this taxon |
| readn_pc | percentage of read pairs assigned to this taxon |
| csum | cumulative read distribution score (percentage of reads mapped to this taxon and more abundant taxa) |
| csumq | confidence score based on csum (1 ~ reliable, 2 ~ intermediate, 3 ~ unreliable) |
| contign | contigs assigned to this taxon |
| species | species name (NCBI taxonomy) |
| genus | genus name |
| family | family name |
| division | NCBI division |
Table 2: Columns in abund_table.xlsx
Contig annotations are printed to contig_annot.xlsx, with separate spreadsheets for viruses (excluding bacteriophages), bacteria, bacteriophages and eukaryotes. Raw data is in contigs_annot.tsv.
| Column | Description |
|---|---|
| search | applied database search (e.g. blastn) |
| db | applied database (e.g. UniRef100.vi) |
| dbtype | nucl for nucleotide, prot for protein databases |
| contig | contig id |
| orf | ORF description in start-end:strand format |
| clen | contig length |
| sseqid | subject sequence id |
| bitscore | alignment score |
| alen | alignment length |
| pident | percent identity |
| qlen | query sequence length |
| qcov | query coverage |
| slen | subject sequence length |
| scov | subject coverage |
| staxid | subject sequence taxid |
| sname | subject sequence name |
| bphage | yes for bacteriophage staxids |
| division | NCBI division |
| species, genus, family, order, class | assigned taxa |
| host.source | host source of the ICTV exemplar species representing this family |
| genome.composition | genome composition of the ICTV exemplar species in this family |
Table 3: Columns in contig_annot.xlsx.
The last two columns come from the ICTV Virus Metadata Resource, which LazypipeX now integrates alongside the NCBI taxonomy. They are useful for triaging a virus list: a hit in a family whose exemplar hosts are plants or insects means something different in a mammalian tissue sample than one in a family of vertebrate viruses.
reports/refgen.report.html opens an Integrative Genomics Viewer report showing where the viral contigs fall on the reference genomes they were assigned to — the quickest way to see whether a hit represents a near-complete genome or a single conserved fragment.
| File | Description |
|---|---|
| figures/read.hist.png | length histogram for reads |
| figures/contigs.hist.png | length histogram for contigs |
| figures/contigs.5-95-100.png | contig length histogram by Q0–Q5, Q5–Q95 and Q95–Q100 percentiles |
Table 4: Quality control plots
Unzip the trimmed reads first:
gunzip -k results/mysample/reads/read*.trim.fq.gz
Then retrieve the reads mapped to a contig, a species, or a taxid:
bin/retrieve_reads -r results/mysample -v -c k99.17
bin/retrieve_reads -r results/mysample -v -s "Circovirus mink"
bin/retrieve_reads -r results/mysample -v -t 1239574
For a set of samples analysed as an array job, batch_sample_summary.pl,batch_abund_summary.pl and batch_annot_summary.pl combine the per-sample results into single spreadsheets. See