---
name: "idseq-bench-score"
section: "1"
platform: "linux"
package: "idseq-bench"
version: "0.0~git20210602.27fb6dc-1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/idseq-bench-score"
---

# idseq-bench-score(1)

Score benchmark samples based on answer key

## NAME

idseq-bench-score - Score benchmark samples based on answer key

## SYNOPSIS

**idseq-bench-score** \[-h\] \[-o OUTPUT\_FILE\] \[-t \[TRUTH\_FILES \[TRUTH\_FILES ...\]\]\] \[-e ENV\] \[-p LOCAL\_PATH\] \[--mono-aupr\] project\_id sample\_id pipeline\_version

## DESCRIPTION

Score benchmark samples based on answer key (against key encode in fastq read IDs for IDseq Bench samples or against a provided answer key).

## OPTIONS

### positional arguments:

- project\_id

  ID of the project

- sample\_id

  ID of the sample

- pipeline\_version

  Pipeline version to retrieve: \<major\>.\<minor\>

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **-o** OUTPUT\_FILE, **--output-file** OUTPUT\_FILE

  Path of output file to write the results to (if not set results are written to stdout)

- **-t** \[TRUTH\_FILES \[TRUTH\_FILES ...\]\], **--truth\_files** \[TRUTH\_FILES \[TRUTH\_FILES ...\]\]

  Space separated list of truth files. Truth files are TSV files with the fields \<tax\_id, absolute abundance, relative abundance, rank, tax\_name\>

- **-e** ENV, **--env** ENV

  String name of environment in which sample exists; options are: prod (default), staging

- **-p** LOCAL\_PATH, **--local-path** LOCAL\_PATH

  Root of local path where IDseq files are stored. Must follow the same structure to store files as IDseq

- **--mono-aupr**

  Computed adjusted AUPR by forcing the precision/recall curve to be monotonic decreasing

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.