raptor build

Table of Contents

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

Main Parameters

-​-input

HIBFIBF

• A layout file produced with raptor layout.
• 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

HIBFIBF

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

-​-window

HIBFIBF

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

-​-fpr

HIBFIBF

• Read from layout file. The read value can be overwritten with this option. However, a warning will be emitted to prevent accidentally overwriting fpr.

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

HIBFIBF

• Read from layout file. The read value can be overwritten with this option. However, a warning will be emitted to prevent accidentally overwriting h.

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

HIBFIBF

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