index

Table of Contents

• raptor search
  • Main Parameters
    • -​-index
    • -​-query
    • -​-output
    • -​-threads
    • -​-quiet
    • -​-error
    • -​-threshold
    • -​-query_length
    • -​-tau
    • -​-p_max
    • -​-cache-thresholds

raptor search

Main Parameters

-​-index

The path to the index. For partitioned indices, the suffix _x, where x is a number, must be omitted.

-​-query

File containing query sequences.

Many file types and compressions are supported. Click to show a list.

Supported file extensions are (possibly followed by bz2, gz, or bgzf):

• embl
• fasta
• fa
• fna
• ffn
• faa
• frn
• fas
• fastq
• fq
• genbank
• gb
• gbk
• sam

-​-output

The output file name.

• Format

  ###<text>                     | Meta-information
  ##<text>                      | Meta-information
  #<number><tab><filepaths>     | Assigns each input file a number. Multiple filepaths are separated by a whitespace
  #QUERY_NAME<tab>USER_BINS     | Header for the results
  <query_id><tab>[<number>...]  | A line for each query, listing matches in input files, if any. Multiple hits are separated by a comma.

• Example

  ### Minimiser parameters
  ## Window size = 19
  ## Shape = 1111111111111111111
  ## Shape size (length) = 19
  ## Shape count (number of 1s) = 19
  ### Search parameters
  ## Query file = "/data/query.fq"
  ## Pattern size = 65
  ## Output file = "search.out"
  ## Threads = 1
  ## tau = 0.9999
  ## p_max = 0.4
  ## Percentage threshold = nan
  ## Errors = 0
  ## Cache thresholds = false
  ### Index parameters
  ## Index = "/data/index.hibf"
  ## Index hashes = 2
  ## Index parts = 1
  ## False positive rate = 0.05
  ## Index is HIBF = true
  #0  /data/bin1.fa
  #1  /data/bin2.fa
  #2  /data/bin3.fa
  #3  /data/bin4.fa
  #QUERY_NAME USER_BINS
  query1  
  query2  1
  query3  0,1,2

-​-threads

The number of threads to use. Sequences in the query file will be processed in parallel. Negligible effect on RAM usage for unpartitioned indices. Moderate effect for partitioned indices.

-​-quiet

By default, runtime and memory statistics are printed to stderr at the end.

This flag disables this behaviour.

-​-error

The number of allowed errors.

Note

Mutually exclusive with –threshold.

-​-threshold

Ratio of k-mers that need to be found for a hit to occur.

Note

Mutually exclusive with –error.

-​-query_length

The sequence length of a query. Used to determine thresholds. The sequence lengths should have little to no variance.

If not provided:

• the median of sequence lengths in the query file is used.
• a warning is emitted if there is a high variance in sequence lengths.
• an error occurs if any sequence is shorter than the window size.

-​-tau

The higher tau, the lower the threshold.

Note

Has no effect when using --threshold or w == k.

-​-p_max

The higher p_max, the higher the threshold.

Note

Has no effect when using --threshold or w == k.

-​-cache-thresholds

Stores the computed thresholds with a unique name next to the index. In the next search call using this option, the stored thresholds are re-used. Two files are stored:

• threshold_*.bin: Depends on query_length, window, kmer/shape, errors, and tau.
• correction_*.bin: Depends on query_length, window, kmer/shape, p_max, and fpr.

Note

Has no effect when using --threshold or w == k.