index

Table of Contents

• raptor prepare
• Main Parameters
  • -​-input
  • -​-output
  • -​-threads
  • -​-quiet
  • -​-kmer
  • -​-window
  • -​-kmer-count-cutoff
  • -​-use-filesize-dependent-cutoff

raptor prepare

Optionally preprocesses files for the use with raptor layout and raptor build.

Can continue where it left off after a crash or in multiple runs.

When to use:

• Applying k-mer filtering based on abundance.

Main Parameters

-​-input

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

-​-output

A path to the output directory. The directory will be created if it does not exist.

Will create a minimiser.list inside the output directory. This file contains a list of generated minimiser files, in the same order as the input. This file can be used as input for raptor layout or raptor build.

Created output files for each input file:

• *.header: Contains the shape, window size, cutoff and minimiser count.
• *.minimiser: Contains binary minimiser values, one minimiser per line.
• *.in_progress: Temporary file to track process. Deleted after finishing computation.

Attention

The window and k-mer sized used for preprocessing are propagated to raptor layout and raptor build and cannot be overwritten there.

Note

If raptor prepare aborts unexpectedly, you can rerun the same command. Files that have already preprocessed will be skipped.

Attention

When you manually delete a .in_progress file, also delete the corresponding .header and .minimiser file.

-​-threads

The number of threads to use. Multiple files will be handled in parallel. While more threads speed up the preprocessing, the RAM usage also increases.

Note

Use less threads if raptor prepare fails due to RAM restrictions.

-​-quiet

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

This flag disables this behaviour.

-​-kmer

See Choosing window and k-mer size.

Attention

This parameter will be used by raptor build and hence should be chosen carefully. The k-mer size cannot be changed afterwards.

-​-window

See Choosing window and k-mer size.

Attention

This parameter will be used by raptor build and hence should be chosen carefully. The window size cannot be changed afterwards.

-​-kmer-count-cutoff

Only store k-mers with at least (>=) x occurrences.

Note

Mutually exclusive with –use-filesize-dependent-cutoff.

-​-use-filesize-dependent-cutoff

Apply cutoffs from Mantis(Pandey et al., 2018).

File size	Cutoff
≤ 300 MiB	1
≤ 500 MiB	3
≤ 1 GiB	10
≤ 3 GiB	20
> 3 GiB	50

File sizes are based of gzipped FASTQ files. Compression reduces the file size by around factor 3. FASTA files are approximately 2 times smaller than FASTQ.

Note

Mutually exclusive with –kmer-count-cutoff.