ABySS ================================================================================
ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.
Please cite our papers.
Contents ================================================================================
- Installation
- Install ABySS using Conda
- Install ABySS using Homebrew
- Install ABySS on Windows
- Dependencies
- Dependencies for linked reads
- Optional dependencies
- Compiling ABySS from source
- Before starting an assembly
- Modes
- Bloom filter mode
- MPI mode (legacy)
- Examples
- Assemble a small synthetic data set
- Assembling a paired-end library
- Assembling multiple libraries
- Scaffolding
- Scaffolding with linked reads
- Rescaffolding with long sequences
- Assembling using a paired de Bruijn graph
- Assembling a strand-specific RNA-Seq library
- Optimizing the parameters k and kc
- Running ABySS on a cluster
- Using the DIDA alignment framework
- Assembly Parameters
- ABySS programs
- Export to SQLite Database
- Database parameters
- Helper programs
- Citation
- Related Publications
- Support
- Authors
Installation ================================================================================
Install ABySS using Conda (recommended)
If you have the Conda package manager (Linux, MacOS) installed, run:
conda install -c bioconda -c conda-forge abyss
Or you can install ABySS in a dedicated environment:
conda create -n abyss-env conda activate abyss-env conda install -c bioconda -c conda-forge abyss
Install ABySS using Homebrew
If you have the Homebrew package manager (Linux, MacOS) installed, run: