CarpeDeam is a damage-aware metagenome assembler for ancient metagenomic DNA datasets. It takes (merged) reads and a damage matrix as input and prooved to work best for heavily damaged datasets. CarpeDeam is built upon PenguiN (https://github.com/soedinglab/plass).
Cite CarpeDeam:
CarpeDeam can be installed via conda, as statically compiled Linux version or by compiling the program from source.
Step 1: Download the static binary. The list of releases is here: https://github.com/LouisPwr/CarpeDeam/tags Each release comes with a static binary. Find the URL of the static binary by right-clicking and selecting "copy link"
wget [URL TO RELEASE BINARY]
# unpack the binary
tar -xvzf carpedeam-static.tar.gz
Where you paste the URL of the binary. If you have root access, simply install the executable by running
sudo cp carpedeam /usr/bin
Otherwise, just leave the executable where it is or copy it in a bin/ directory in your home directory:
mkdir -P $HOME/bin/
cp carpedeam $HOME/bin/
Step 2: Mark the binary executable:
chmod +x carpedeam
Install Conda (https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) and Bioconda (https://bioconda.github.io/) and type the following:
conda install -c bioconda carpedeam
Thanks to martin-g for the bioconda support!
Compiling CarpeDeam from source optimizes it for your specific system, potentially boosting performance.
Prerequisites:
- Git
- G++ (version 4.6 or higher)
- CMake (version 3.0 or higher)
After compilation, find the carpedeam binary in the build/bin directory.
git clone https://github.com/LouisPwr/CarpeDeam
cd CarpeDeam
git submodule update --init
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
make -j 4 && make install
export PATH="$(pwd)/bin/:$PATH"
If you want the program to be permanently available, you can add the full path to the carpedeam binary to your .bashrc file. Don't forget to source it afterward. Open your ~/.bashrc and add the following line anywhere:
export PATH="/home/path/to/carpedeam/build/bin:$PATH"
Refresh your "~/.bashrc":
source ~/.bashrc
When compiling from source, CarpeDeam requires zlib and bzip.
CarpeDeam needs roughly 1 byte of memory per residue to work efficiently. CarpeDeam will scale its memory consumption based on the available main memory of the machine. CarpeDeam needs a CPU with at least the SSE4.1 instruction set to run.
We recommend merging reads before assembly as merging improves read quality. You need to supply a damage matrix (format see FAQ) to actually make it work.
# assemble merged reads
carpedeam ancient_assemble examples/reads.fastq.gz assembly.fasta tmp --ancient-damage /path/to/damage/prefix
Important parameters:
--ancient-damage Path to damage matrix. Must be tab separated file (format see FAQ)
--num-iter-reads-only Number of iterations which use raw-reads only (=sequences that have not been extended yet); damage aware; results in short (<500bp) but precise contigs; we suggest 3 to 5 iterations
--num-iterations Number of total iterations (= iterations of read-only-extension + iterations of contig-merging); somewhat damage aware; results in long contigs; we suggest 9 to 12 iterations (includes the number of num-iter-reads-only)
--min-merge-seq-id Minimum sequence identity threshold of overlapping sequences in contig-merging-step (=after correction). Lower than 99% will result in even longer contigs, but increases the risk of misassemblies
--unsafe Turn on to maximize contig lengths and sensitivity. Comes with a higher risk of assembling more chimeric contigs. Default OFF [0].
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Which format does the damage matrix need to have? (Template see example dir in this repository)
It must be a tab seperated file with a header line for the individual substitutions and one line per position. The C-to-T substitutions start at position 1 of the five-prime-end, the G-to-A substitutions start at position 1 of the three-prime-end.
Important: The damage matrices need to have the suffix 3p.prof and 5p.prof
myDamage_5p.prof could look like:
A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G 0 0 0 0 0 0.329405 0 0 0 0 0 0 0 0 0 0 0 0.221745 0 0 0 0 0 0 0 0 0 0 0 0.187678 0 0 0 0 0 0 0 0 0 0 0 0.161196 0 0 0 0 0 0 0 0 0 0 0 0.144011 0 0 0 0 0 0myDamage_3p.prof could look like:
A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G 0 0 0 0 0 0 0.32891 0 0 0 0 0 0 0 0 0 0 0 0.223405 0 0 0 0 0 0 0 0 0 0 0 0.188599 0 0 0 0 0 0 0 0 0 0 0 0.164419 0 0 0 0 0 0 0 0 0 0 0 0.146352 0 0 0 0 0 -
Do all other substitution rates have to be 0?
No, but focusing on C-to-T and G-to-A substitutions is the best approach (for now):
Typical ancient DNA damage: C-to-T and G-to-A are the most common substitutions in ancient DNA. These are primarily caused by chemical processes over time, not evolution.
Other substitution types: Non-zero rates for other substitutions usually indicate evolutionary changes or sequencing errors (among others). Including these could increase the risk of assembly errors.
Focusing on C-to-T and G-to-A helps avoid incorrect "corrections" and ensures more accurate species-specific assembly.
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How do I correctly porvide the damage matrix file path? Assume our damage matrices are located at:
/path/to/emotional/damage/sampleDamage_3p.prof /path/to/emotional/damage/sampleDamage_5p.profThe you can call CarpeDeam as follows:
carpedeam ancient_assemble myInput.fasta myOutput.fasta tmpDir --ancient-damage /path/to/emotional/damage/sampleDamage_