To compile and install ABySS in /usr/local. See "Compiling ABySS from source" for further steps. To generate the configure script and make files. When installing ABySS from GitHub source the following tools are required: Dependencies for linked readsīrew install brewsci/bio/arcs brewsci/bio/links-scaffolder Later versions of Boost compile without error. In='test-data/reads1.fastq test-data/reads2.fastq' Calculate assembly contiguity statistics abyss-fac test-unitigs.fa Dependenciesĭependencies may be installed using the package manager Homebrew on macOS and Linxubrew on Linux and Windows, using Windows Subsystem for Linux.ĪBySS requires a C++ compiler that supports OpenMP such as GCC.īrew install boost open-mpi google-sparsehashĪBySS will receive an error when compiling with Boost 1.51.0 or 1.52.0 since they contain a bug. Run the command sudo apt-get install abyss Assemble a small synthetic data set wget Install Windows Subsystem for Linux and Linuxbrew, and run the command brew install abyss Install ABySS on Debian or Ubuntu Install Homebrew, and run the command brew install abyss Install ABySS on Windows Install Linuxbrew, and run the command brew install abyss Install ABySS on macOS Assembling a strand-specific RNA-Seq library.Assembling using a paired de Bruijn graph.Assembling using a Bloom filter de Bruijn graph.Contact the project lead (Inanc Birol) (ibirol at bcgsc dot ca?subject=abyss%20developer%20position) Contents Inquire for staff, graduate student, and postdoctoral positions. Looking for a fun & worthy challenge? Think you can contribute code to this project? Join our team of developers! We are currently looking for C++ bioinformatics programmers. ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.
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