The Alice Assembler

The Alice assembler is named after the character of Lewis Caroll's Alice in Wonderland, and more precisely to the "drink-me potion" and "eat-me cake", which make Alice respectively shrink and grow. The idea of the Alice assembler is to shrink the input reads, perform assembly on shrunken data and inflate the obtained assembly back to normal size. The compression is a Mapping-friendly Sequence Reduction (MSR) of high order, which allows all base to be taken into account during compression. However, it increases error rate of the reads. It is thus recommended to run it on long and accurate reads.

Installation

Dependencies: numpy, scipy, cmake

To have all the dependencies, it is advised to create first a conda environment with all the dependencies (bcalm, minimap2, openmp, g++, scipy, numpy)

conda create -n hairsplitter -c bioconda -c conda-forge bcalm openmp libgomp gxx gcc scipy numpy cmake
conda activate hairsplitter

Then download and compile the Alice assembler

git clone https://github.com/RolandFaure/Alice-asm.git
cd Alice-asm
mkdir build && cd build
cmake ..
make

Usage

SYNOPSIS
        aliceasm -r [<i>] -o [<o>] [-t [<t>]] [-m [<m>]] [-l [<o>]] [-c [<c>]]
            [--bcalm [<b>]] [--minimap2 [<m>]] [-v]

OPTIONS
        -r, --reads input file (fasta/q)
        -o, --output
                    output file (gfa)

        -t, --threads
                    number of threads [1]

        -m, --min-abundance
                    minimum abundance of kmer to consider solid [10]

        -l, --order order of MSR compression (odd) [201]
        -c, --compression
                    compression factor [20]

        --bcalm     path to bcalm [bcalm]
        --minimap2  path to minimap2 [minimap2]
        -v, --version
                    print version and exit