Downloads¶
Save the output appropriate to your next step. A private results link restores a job for seven days; it is not a permanent file archive. Tool-specific downloads are available after Open results from My Jobs.
| Tool | Download | Contents and use |
|---|---|---|
| SeqFetcher | FASTA | Selected full-length records, deduplicated by returned accession. An assembly contains multiple contigs in one FASTA. |
| SeqFetcher | Metadata TSV / ZIP | Selected metadata; ZIP adds combined/per-accession FASTA, metadata JSON, run report and failed/pending ID lists. |
| CRISPRPrep | CRISPRCasFinder JSON | Generated detector output, available for detection jobs. Retains detector annotations. Re-import treats the file as one sample; preserve the initial processed CSV for multi-sample jobs. Uploaded source JSON must be kept separately. |
| CRISPRPrep | Unprocessed CSV | spacers_unprocessed.csv: spacer rows after evidence/count filtering, before direction/N normalization. |
| CRISPRPrep | Processed CSV | spacers_processed.csv: filtered/normalized rows and reverse-complement/effective-repeat fields. Use in SpacerMap, CRISPRPhylo or SpacerTarget. |
| CRISPRPrep | Processing report | Counts, warnings, array outcomes and retrieval failures where applicable. Saved processing options are omitted; record them separately. |
| SpacerMap | Download numbered file | Tab-separated Spacer_ID / Spacer_Sequence lookup in a .txt file. Retains distinct sequence variants per ID, but has no array membership or order. Use the array-map SVG or restored export_text for array reuse. |
| SpacerMap | SVG / raster image | Array diagram; supported SVG carries editable array metadata. PNG/JPEG/TIFF/WEBP use the chosen DPI. |
| SpacerMap | Cluster-network SVG / PNG | Network drawing from the cluster preview's own download buttons. |
| SpacerMap | Download statistics CSV | SpacerMap-occurrence.csv: all IDs and the number of arrays containing each; repeated copies within one array count once. |
| SpacerMap | Occurrence SVG / PDF / EPS / PNG / JPG / TIFF / WEBP | Complete bar chart and presence/absence matrix for 1–50 distinct IDs. Separate from the array-map SVG; cannot be imported into ArrayPhyloViz as array data. |
| CRISPRPhylo | Download .nwk | Current displayed tree, including local rerooting. My Jobs' direct tree download retains the original inferred root. |
| CRISPRPhylo | Download tree | SVG or PNG of the complete current strain tree, independent of zoom/pan. |
| CRISPRPhylo | Download array trees (.zip) | Optional group Newick files, index.csv, labels.csv and README.txt; enable before running. Not included inside the result JSON. |
| SpacerTarget | Export filtered TSV | Match rows passing current table filters and node/edge focus, across all table pages. |
| SpacerTarget | All candidates TSV | All returned alignments without Strict/current table filtering; not an exhaustive database search. |
| SpacerTarget | Search report | Retained query/occurrence identifiers, match evidence, annotation status and batch history. Terminal reports omit original full sequences, parameters and raw BLAST responses. |
| SpacerTarget | PNG / SVG | Current association network view. Preserve TSV/report as supporting evidence. |
| ArrayPhyloViz | Save project | Editable local project JSON with mapping, tree, styles, array merging/order and figure edits. |
| ArrayPhyloViz | Save changes | A server snapshot of the project with its own ID and expiry; later edits require another save. |
| ArrayPhyloViz | Mapping TSV | Array-to-leaf assignments, spacer counts and displayed reversals. |
| ArrayPhyloViz | SVG / PNG / PDF | Complete integrated figure. SVG embeds project data; PDF is downloaded directly and is not a replacement for the editable JSON. |
| ArrayPhyloViz | Newick | Full tree in edited child order, using original names and branch lengths. Display annotations live in the project. |
| My Jobs | Export job links | Plain-text links for importing history on another device; no sequence data or figures are included. |
Does a visible filter affect downloads?¶
| Tool | Scope |
|---|---|
| SeqFetcher | Selected retrieved rows, including selected rows hidden by search. The header checkbox affects only visible rows. |
| CRISPRPrep | All rows produced by the run's processing settings, regardless of preview search/page. |
| SpacerTarget | Filtered TSV follows table filters and graph focus; All candidates ignores them. Network type-visibility checkboxes affect the drawing only. |
| SpacerMap | Array-map export contains the complete diagram. Statistics CSV includes all IDs, beyond the first 100 table rows; occurrence charts include every ID only when there are 1–50 in total. |
| CRISPRPhylo | Complete figure, independent of preview zoom/pan, using the current local root. |
| ArrayPhyloViz | Complete figure at selected export resolution; collapsed clades and styles affect the drawing. |
SpacerTarget table rows count occurrence–site matches; network edge weights count different supporting query sequences. Those totals need not agree. After input cleanup, the TSV sequence column can be blank while alignment evidence remains; keep original input FASTA/CSV for complete spacer sequences.
SpacerMap occurrence figures use their own format/DPI controls. Raster occurrence exports are capped at 40 million pixels; lower DPI or choose SVG/PDF if necessary. Vector export does not remove the 50-ID chart limit. Archive normalized array text or the array-map SVG with the statistics CSV to preserve array membership and the ID scheme. The separate ID–sequence lookup does not preserve membership.
Minimum analysis bundle¶
Keep original accessions/FASTA/JSON, sample identities, a separate settings record, processing report, processed CSV, normalized array text or array-map SVG, ID–sequence lookup, occurrence CSV/figures when used, original and any rerooted Newick, optional array-tree ZIP, figure mapping/project and final images. For target searches add original spacers, database/hit limit/filter settings, all candidates, filtered TSV and search report.
Record analysis date and software version when available, method/profile, repeat-distance value, processing thresholds, alignment/clustering, color seed and relevant figure edits. Server reports omit some input-related fields by design; do not rely on a result link alone to reproduce an analysis.