Read-Level Results

Return a URL with which the read-level results for the classification may be downloaded. Note that the CLI automatically downloads the read-level results TSV file when using the --read-level flag. The read-level results may be downloaded in the One Codex web application on the righthand side of each analysis page:

The resulting gzipped TSV file will typically have the following columns (note that these are the standard fields for One Codex Database results but are not guaranteed to be stable and may differ for, e.g., different underlying databases and classifiers):

Property	Description
Header string	The FASTA or FASTQ header for the record. In practice these should match the input order of the FASTA/Q file, though this is not strictly guaranteed. _Note: This column exists for all analyses run before June 2017 but is discontinued in current and future analyses. We strongly recommend that any code indexing a results TSV uses the column headers to determine the position of relevant data rather than assuming a given column order and position._
Tax ID string	The taxonomy ID the read is assigned to. Note that this is a read-level assignment that does not incorporate global sample-wide information. This column exists for all results.
N Hits int	The number of k-mers found in the input read against the target database. This column exists for all k-mer based classification results.
Seq Len int	The length of the read or contig. This column exists for all results.
Passed Filter boolean/string	Whether the read passed a sample-wide filter. `T` indicates True and `F` indicates False. Reads not passing the filter may be erroneously assigned based on adapters, stacking artifacts, and other errors and should generally be ignored. This column exists for any results where global, sample-wide filtering is applied. All One Codex database results since April 2016 have included this field (details).
Kmer Chain string	A sequence of `:`-separated taxonomy IDs (`tax_id`) and position (`pos`) pairs (e.g., `543:10`) indicating the starting positions of all contiguous series of hits within the input read. Transitions between different taxonomy IDs are separated with a `\|`. – The sample string `543:1\|562:22\|0:25`, indicates that all of the k-mers beginning at position `1` through `21` map to the NCBI taxonomy ID `543` (Enterobacteriaceae), all k-mers beginning at position `22` through position `24` map to `562` (E. coli), and the k-mers beginning at position `25` through the end of the input read have no hits. _Note: This column exists for all analyses run before June 2017 but is discontinued in current and future analyses. Note: The special value `0` is used to indicate no hit. `1` represents the root of the taxonomic tree._