StringDecomposer

Version 1.1.2

As an input StringDecomposer algorithm takes the set of monomers (typically, alpha satellites) and a genomic segment (assembly, Oxford Nanopore or a PacBio HiFi read) that contains a tandem repeat consisting of the given monomers. StringDecomposer partitions this segment into distinct monomers, providing an accurate translation from the nucleotide alphabet into the monomer alphabet.

Installation

The recommended way to install StringDecomposer is with conda package manager:

conda install -c bioconda stringdecomposer

Alternatively, StringDecomposer can be build and installed from source.

Requirements:

Python3.5+
g++ (version 5.3.1 or higher)

The required python packages can be installed through conda using

conda install --file requirements.txt

Local building without installation:

git clone https://github.com/ablab/stringdecomposer.git
cd stringdecomposer
make

Then, StringDecomposer is available as

bin/stringdecomposer

Installing from source:

git clone https://github.com/ablab/stringdecomposer.git
cd stringdecomposer
make install

Then, StringDecomposer is available as

stringdecomposer

Removal of StringDecomposer installed from source:

make uninstall

Quick start

The following command assumes that StringDecomposer is either installed through conda or from source.

stringdecomposer ./stringdecomposer/test_data/read.fa ./stringdecomposer/test_data/DXZ1_star_monomers.fa -o ./stringdecomposer/test_data

The same result can be achieved with make test_launch (for local build without installation) and make test_launch_install (for installed from source or via conda). These make rules ensure correctness of StringDecomposer's output on the test dataset.

In case StringDecomposer is built locally, the command that achieves the same result is

./bin/stringdecomposer ./stringdecomposer/test_data/read.fa ./stringdecomposer/test_data/DXZ1_star_monomers.fa -o ./stringdecomposer/test_data

Results can be found in

./stringdecomposer/test_data/final_decomposition.tsv           final decomposition of sequences to monomer alphabet
./stringdecomposer/test_data/final_decomposition_alt.tsv       final decomposition of sequences to monomer alphabet with alternative monomers for each position
./stringdecomposer/test_data/final_decomposition_raw.tsv       raw decomposition with initial dynamic programming scores instead of identities

Each line in final_decomposition.tsv file has the following form:

<read-name> <best-monomer> <start-pos> <end-pos> <identity> <second-best-monomer> <second-best-monomer-identity> <homo-best-monomer> <homo-identity> <homo-second-best-monomer> <homo-second-best-monomer-identity> <reliability>

homo-related columns represent statistics of the best-scoring (second-best-scoring) monomer after compression of homopolymer runs in both the monomer and the target read. Reliability is either equal to ? (signifies unreliable alignment which can be caused by a retrotransposon insertion or a poor quality segment of a read) or + (if the alignment is reliable). The columns <second-best-monomer>, <second-best-monomer-identity>, <reliability>, and _homo_-related columns will have values None and -1 unless the user supplies the argument --second-best (see Synopsis below).

Synopsis

stringdecomposer [-h] [-t THREADS] [-o OUT_FILE] [-i MIN_IDENTITY] [-s SCORING] [-b BATCH_SIZE] [--second-best] sequences monomers

Required arguments:

sequences                                         fasta-file with long reads or genomic sequences (accepts multiple sequences in one file)
monomers                                          fasta-file with monomers

Optional arguments:

-h, --help                                         show this help message and exit

-t THREADS, --threads THREADS                      number of threads (by default 1)

-o OUT_FILE, --out-file OUT_FILE                   output tsv-file (by default final_decomposition.tsv)

-i MIN_IDENTITY, --min-identity MIN_IDENTITY       only monomer alignments with percent identity >= MIN_IDENTITY are printed (by default MIN_IDENTITY=0%)

-s SCORING, --scoring SCORING                      set scoring scheme for StringDecomposer in the format "insertion,deletion,mismatch,match" (by default "-1,-1,-1,1")

-b BATCH_SIZE, --batch-size BATCH_SIZE             set size of the batch in parallelization (by default 5000)

--second-best                                      StringDecomposer will generate <second-best-monomer>, <second-best-monomer-identity>, <reliability> and _homo_-related columns (not recommended when running StringDecomposer of a large number of monomers)

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