Alice is a genomic and metagenomic assembler designed for HiFi read (<0.1% error rate).
It 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.
The recommended way to install Alice is through conda
conda install -c bioconda aliceasm
To download and compile the Alice assembler from source
git clone https://github.com/RolandFaure/Alice-asm.git
cd Alice-asm
mkdir build && cd build
cmake ..
make
/build/aliceasm --help
_______ _ _ _ _ _
|__ __| | /\ | (_) /\ | | | |
| | | |__ ___ / \ | |_ ___ ___ / \ ___ ___ ___ _ __ ___ | |__ | | ___ _ __ :: _.mnm._
| | | '_ \ / _ \ / /\ \ | | |/ __/ _ \ / /\ \ / __/ __|/ _ \ '_ ` _ \| '_ \| |/ _ \ '__| : : ( _____ )
| | | | | | __/ / ____ \| | | (_| __/ / ____ \\__ \__ \ __/ | | | | | |_) | | __/ | : : | |
|_| |_| |_|\___| /_/ \_\_|_|\___\___| /_/ \_\___/___/\___|_| |_| |_|_.__/|_|\___|_| :__: `___/
Command line: ./build/aliceasm --help
Alice Assembler version 0.6.41
Last update: 2025-07-09
Author: Roland Faure
Help:
SYNOPSIS
./build/aliceasm -r [<r>] -o [<o>] [-t [<t>]] [-l [<o>]] [-c [<c>]] [-H] [-m [<m>]] [-k
[<k>]] [--single-genome] [--bcalm [<b>]] [--clean] [--test [<t>]] [-v] [-h]
OPTIONS
-r, --reads input file (fasta/q)
-o, --output
output folder
-t, --threads
number of threads [1]
-l, --order order of MSR compression (odd) [101]
-c, --compression
compression factor [20]
-H, --no-hpc
turn off homopolymer compression
-m, --min-abundance
minimum abundance of kmer to consider solid - RECOMMENDED to set to coverage/2
if single-genome [5]
-k, --kmer-sizes
comma-separated increasing sizes of k for assembly, must go at least to 31
[17,31]
--single-genome
Switch on if assembling a single genome
--bcalm path to bcalm [bcalm]
--clean remove the tmp folder at the end [off]
-v, --version
print version and exit
-h, --help print this help message and exit
Let's run an assembly together. Let's imagine that we want to assemble SRR21295163 as a metagenome (even though it is a single E.coli genome, but lets keep the files small for this section)
First, download the dataset:
fastq-dump SRR21295163
Then assemble
conda activate aliceasm #Don't forget to place yourself in an environment with the bcalm dependency, e.g. the bioconda::aliceasm conda package
aliceasm -r SRR21295163.fastq -o output_assembly -t 8
On my computer, the assembly completed in 25s and 0.33GB RAM. You should have created an output_assembly folder, containing assembly.gfa and assembly.fasta (which represent exactly the same contigs). If you want to make sure the assembly was successful, the assembly I obtained is available on this repo, in test/SRR21295163_assembly.gfa.
Yes! If you are trying to assemble a single genome, it is recommended to use flag --single-genome and set -m to expected-coverage/2 in order to simplify the output graph.
Please cite the preprint: https://www.biorxiv.org/content/10.1101/2025.09.29.679204v1