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Chopper - partition your sequences build status codecov

System requirements

  • GCC Version >= 11
  • CMake Version >= 3.18

General setup

Set up the repository:

git clone --recurse-submodules https://github.com/seqan/chopper

Set up the build directory

mkdir chopper_build
cd chopper_build
cmake ../chopper

Build chopper

make

Optional: Build the test to check if everything works

make test

In case anything fails, please open a GitHub issue mentioning your OS and compiler version.

Chopper

Chopper uses a hierarchical DP algorithm to layout user bins into a given number of technical bins, optimizing the space consumption of a Hierarchical Interleaved Bloom Filter (HIBF).

Chopper needs an input file with filenames. The file could look like this: (it is always good to give absolute instead of relative paths)

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

You can then run chopper with the following command:

./chopper --input-file data.tsv --kmer-size 21 --output-filename chopper.layout

There are more options to tweak the layout (with sensible defaults). You get detailed information if you run:

./chopper --help

The resulting layout file can be used to build an HIBF index with raptor.

Understanding the layout file

There is no need to actually understand the internals of the layout file, as you can just let raptor build the HIBF index automatically from the layout. If you are interested, or you have a specific use case, here is some information about the layout.

A layout file has 3 parts: (1) The config, (2) the header, (3) the layout content.

At first, the config of chopper that created this particular file is stored. The config part is identified by two hashes ## at the beginning of each line. It starts with ##CONFIG and ends with ##ENDCONFIG. It could look like this:

##CONFIG:
##{
##    "config": {
##        "version": 2,
##        "k": 19,

...

##ENDCONFIG

The config is followed by the actual header of the layout file, which stores important information for building the HIBF index. The header is identified by one hash # at the beginning of each line. It starts with #HIGH_LEVEL_IBF max_bin_id:[X] and ends with #FILES BIN_INDICES NUMBER_OF_BINS, the column names of the layout content.

It could look like this:

#HIGH_LEVEL_IBF max_bin_id:14
#MERGED_BIN_0 max_bin_id:0
#MERGED_BIN_5;3 max_bin_id:2

...

#FILES	BIN_INDICES	NUMBER_OF_BINS

Each line corresponds to one IBF in the hierarchy, identifying the maximum technical bin, maximal in its k-mer content. This information is needed to compute the size of each IBF when building the HIBF.

Details:

  1. HIGH_LEVEL_IBF max_bin_id:[X]: Reports the id ([X]) of that technical bin in the Top/High level IBF that has the highest kmer content.
  2. MERGED_BIN_[Y] max_bin_id:[X]: Reports the id ([X]) of that technical bin in the IBF identified by [Y].

Following the header, the layout content describes the actual layout. Each line reports the structure for a particular user bin. In that sense, the number of content lines is exactly the same that of the inputs.

It could look like this:

/path/to/file1.fa	12	3
/path/to/file2.fa	0;2	1;1
/path/to/file3.fa.gz	5;4	1;7

...

Columns of the layout content:

  1. FILES: The file path(s) for the user bin.
  2. BIN_INDICES: The technical bin indices on each level that the user bin is stored in. In the example: * file1.fa is stored in technical bin 12 of the top level IBF. * file2.fa is stored in technical bin 0 of the top level IBF which is a merged bin, so it's also stored in a lower level IBF. In this lower level IBF, it is stored in technical bin 2. * file3.fa.gz is stored in technical bin 5 of the top level IBF which is a merged bin so it's also stored in a lower level IBF. In this lower level IBF, it is stored in technical bin 4.
  3. NUMBER_OF_BINS: The number of technical bins the user bin is stored in on each level. For this example: * file1.fa split into 3 technical bins (ids:12,13,14) on the top level IBF. * file2.fa is stored in a merged bin (1) and in a single bin (1) on the lower level. * file3.fa.gz is stored in a merged bin (1) and is split into 7 bins (ids:4,5,6,7,8,9,10) on the lower level.

Multiple files per user bin

Currently, chopper always has a 1-to-1 relation between files and user bins when laying out. If you want to assign multiple files to a user bin, you can use raptor.

raptor prepare also handles files like this:

/path/to/file1-a.fa;/path/to/file1-b.fa;/path/to/file1-c.fa
/path/to/file2.fa
/path/to/file3.fa.gz

...

copper or alternatively raptor layout (which calls chopper) then computes the layout based on the precomputed files.