- GCC Version >= 10
- CMake Version >= 3.15
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 the test to check if everything works
make test
This submodule uses a hierarchical DP algorithm to layout user bins into a given number technical bins, optimizing the space consumption of a Hierarchical Binning Directory.
The app chopper layout
needs an input file with filenames and weights as input
(see chopper count if you want to use kmer counts as weights).
The file has to be tab separated and looks like this:
file_path1 500
file_path2 1000
file_path3 10
...
It can also contain meta information like taxonomic ids which you can group by later on:
file_path1 500 taxID_1
file_path2 1000 taxID_2
file_path2 10 taxID_2
...
If you have the file you can use chopper layout
like this:
./chopper layout -f fata.tsv --technical-bins 2 -o output_filename.txt
Given the example tsv file with the 3 lines above, it will create a file output_filename.txt
which looks like this:
#MERGED_BIN_0 max_bin_id:0
#HIGH_LEVEL_IBF max_bin_id:SPLIT_BIN_1
#BIN_ID SEQ_IDS NUM_TECHNICAL_BINS ESTIMATED_MAX_TB_SIZE
MERGED_BIN_0_0 file_path1 62 9
MERGED_BIN_0_62 file_path2 2 5
SPLIT_BIN_1 file_path2 1 1000
Every line that starts with #
is a header line and is needed for chopper split
and chopper build
.
The output file has the following columns:
BIN_ID
: An identification of the bin. MERGED/SPLIT indicates a bin that has been merged/split. Note that MERGED bins with the same number belong together. In the exampleMERGED_BIN_0_0
andMERGED_BIN_0_62
both belong toMERGED_BIN_0
.SEQ_IDS
: The file paths that belong to this bin.NUM_TECHNICAL_BINS
: The number of technical bins. For SPLIT bins, this indicates the number of technical bins in the High-Level IBF. For MERGED bins, this indicates the number of technical bins in the Low-Level IBF (MERGED bins have always exactly one bin in the High-Level IBF).ESTIMATED_MAX_TB_SIZE
: The estimated maximum bin size of this bin (can be neglected and is used for internal calculations).
More Examples and descriptions will follow soon.