MuCHSALSA

Multi-Core Hybrid Short- And Long-read Sequence Assembler

Based on: Gatter, T., von Löhneysen, S., Fallmann, J. et al. LazyB: fast and cheap genome assembly. Algorithms Mol Biol 16, 8 (2021).

Prerequisites

MuCHSALSA requires the following tools to be available in the PATH:

• jellyfish 2
• bbduk
• Abyss 2 (using 'abyss-pe')
• minimap2
• Python 3.6.9 (at least), including:
  • numpy
  • networkx
  • biopython

Download

A zip file containing a statically linked binary for x86-64 alongside with the assembly pipeline and associated scripts can be downloaded from the releases page on GitHub.

Usage

The pipeline can be run using the following command:

sh pipeline.sh [k-mer-size-filter] [k-mer-size-assembly] [name] [illumina-inputfile-1] [illumina-inputfile-2] [nanopore-inputfile] [output-folder]

Note: The level of parallelization used for parts (default value: 8) of the pipeline is set via a variable in pipeline.sh.

[k-mer-size-filter] specifies the k-mer size for k-mer counting in raw illumina data. Reads with highly abundant k-mers are removed from the data. Starting at k=50 is recommended.

[k-mer-size-assembly] specifies the k-mer size during illumina assembly (here using Abyss). Starting at k=90 is recommended.

Building

Building the project requires git, cmake, clang-15, libc++-15, Doxygen, and Graphviz and can be done by running the following commands:

mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make

If you want to link libc++ statically:

mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DENABLE_BUILD_FAT_EXE=1 ..
make

Tests can be executed by running the following command afterwards:

make test

The library documentation can be built using the command:

make doc

Formatting

All the code within this project is uniformly formatted using clang-format:

find . -regex '.*\.\(cpp\|h\)' -exec clang-format-15 -style=file -i {} \;

Standard Library

This project uses libc++-15 as standard library. For information on installing the LLVM ecosystem see here.