index

Table of Contents

• raptor build
• Main Parameters
  • -​-input
  • -​-output
  • -​-threads
  • -​-quiet
  • -​-kmer
  • -​-window
  • -​-fpr
  • -​-hash
  • -​-parts

raptor build

Main Parameters

-​-input

• HIBF A layout file produced with raptor layout.
• IBF List of sequence files
  The input file contains paths to the sequence data. Each line may contain multiple paths (separated by a whitespace).

  /absolute/path/to/file1.fasta /absolute/path/to/file2.fasta
  /absolute/path/to/file3.fa.gz

  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

  List of preprocessed files
  See -​-output.

  Note

  As a convenience, raptor prepare creates a minimiser.list file in the output directory. This file can be used as input for raptor layout and raptor build.

-​-output

The output file name.

-​-threads

The number of threads to use. Both IBF and HIBF construction can heavily benefit from parallelisation.

-​-quiet

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

This flag disables this behaviour.

-​-kmer

• HIBF Read from layout file. The read value can be overwritten with this option. However, a warning will be emitted to prevent accidentally overwriting k.
• IBF See Choosing window and k-mer size.

-​-window

• HIBF Read from layout file. The read value can be overwritten with this option. However, a warning will be emitted to prevent accidentally overwriting w.
• IBF See Choosing window and k-mer size.

-​-fpr

• HIBF Read from layout file. The read value can be overwritten with this option. However, a warning will be emitted to prevent accidentally overwriting fpr.
• IBF Sets an upper bound for Bloom Filter false positives.
  Recommendation: default value (0.05)
    • A lower fpr limits the number of false-positive results, but increases index size.
    • A higher fpr can help to reduce memory consumption in cases where false-positive k-mers have little effect.
  See also: Bloom Filter Calculator.

Bloom Filter Calculator

-​-hash

• HIBF Read from layout file. The read value can be overwritten with this option. However, a warning will be emitted to prevent accidentally overwriting h.
• IBF The number of hash functions to use for Bloom Filters. Influences the index size.
  Recommendation: default value (2)
  It should only be changed for experimentation.
  See also: Bloom Filter Calculator.

-​-parts

• HIBF Not yet available.
• IBF Splits the index. Lower memory consumption, but higher runtime cost when searching. Output files will have a suffix _x, where x is a number.