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
SYNOPSIS
./aliceasm -r [<r>] -o [<o>] [-t [<t>]] [-l [<o>]] [-c [<c>]] [-H] [-m [<m>]] [-k [<k>]]
[--contiguity] [--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 [5]
-k, --kmer-sizes
comma-separated increasing sizes of k for assembly, must go at least to 31
[17,31]
--contiguity
Favor contiguity over recovery of rare strains [off]
--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
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.