How to install and use Abyss

This article mainly explains "how to install and use Abyss". The content in the article is simple and clear, easy to learn and understand. Please follow the editor's train of thought to study and learn "how to install and use Abyss".

The mainstream NGS genome assembly software first divides the sequence into kmer, and then obtains the assembled sequence based on de Bruijn Graph graph theory algorithm. When the program runs, the kmer string is stored in memory, so the computer's memory is required to be large enough.

Abyss is based on Bloom filter and does not store strings directly, reducing memory consumption.

The installation process is as follows

Wget https://github.com/bcgsc/abyss/releases/download/2.1.0/abyss-2.1.0.tar.gztar xzvf abyss-2.1.0.tar.gzcd abyss-2.1.0/./configure-prefix=$ (pwd)-without-sparsehashmake

After compiling successfully, many executables are generated, which are scattered in different directories. To run the software successfully, you need to add these executables to the PATH environment variable, as follows

Export ABYSS_HOME=/soft/abyss-2.1.0export PATH=$ABYSS_HOME/ABYSS:$PATHexport PATH=$ABYSS_HOME/AdjList:$PATHexport PATH=$ABYSS_HOME/Align:$PATHexport PATH=$ABYSS_HOME/bin:$PATHexport PATH=$ABYSS_HOME/Bloom:$PATHexport PATH=$ABYSS_HOME/BloomDBG:$PATHexport PATH=$ABYSS_HOME/Consensus:$PATHexport PATH=$ABYSS_HOME/DAssembler:$PATHexport PATH=$ABYSS_HOME/DataBase:$PATHexport PATH=$ABYSS_HOME/dialign:$PATHexport PATH=$ABYSS_HOME/DistanceEst:$PATHexport PATH=$ABYSS_HOME/FilterGraph/:$PATHexport PATH=$ABYSS_HOME/FMIndex/:$PATHexport PATH=$ABYSS_HOME/GapFiller:$PATHexport PATH=$ABYSS_HOME/Graph: $PATHexport PATH=$ABYSS_HOME/KAligner:$PATHexport PATH=$ABYSS_HOME/kmerprint:$PATHexport PATH=$ABYSS_HOME/Konnector:$PATHexport PATH=$ABYSS_HOME/Layoutp:$PATHexport PATH=$ABYSS_HOME/LogKmerCountr:$PATHexport PATH=$ABYSS_HOME/Map:$PATHexport PATH=$ABYSS_HOME/MergePaths:$PATHexport PATH=$ABYSS_HOME/Overlap:$PATHexport PATH=$ABYSS_HOME/PairedDBG:$PATHexport PATH=$ABYSS_HOME/ParseAligns:$PATHexport PATH=$ABYSS_HOME/PathOverlap:$PATHexport PATH=$ABYSS_HOME/PopBubbles:$PATHexport PATH=$ABYSS_HOME/Scaffold:$PATHexport PATH=$ABYSS_HOME/Sealer:$PATHexport PATH=$ABYSS_HOME/SimpleGraph:$PATH

Just adjust ABYSS_HOME and set it to the actual directory where the software is located. You can set the above environment variable in the ~ / .bahsrc file, and then run the following code

Source ~. Bahsrc

In this way, the environment variables will take effect, and only then will the software be considered to be installed successfully. The official website also provides a test dataset. The method to download the test dataset is as follows

Wget http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.3.4/test-data.tar.gztar xzvf test-data.tar.gztree-L 1 test-data ├── reads1.fastq └── reads2.fastq

The test data set is a result file of double-ended sequencing. The command to assemble with Abyss is as follows

Abyss-pe Kraft 25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'

The name parameter is the prefix of the generated file. After running, many files will be generated. Here are two files that we are most concerned about.

Test-contigs.fa

Test-scaffolds.fa

Correspond to the results of contig and scaffold respectively.

For Abyss, multiple kmer gradient assemblies can only be achieved through for loops, as follows

For k in `seq 50 8 90`; do mkdir Kingsk abyss-pe-C Kenzk name=test Kaoyuk in=reads.fadone thank you for reading. The above is the content of "how to install and use Abyss". After the study of this article, I believe you have a deeper understanding of how to install and use Abyss, and the specific use needs to be verified in practice. Here is, the editor will push for you more related knowledge points of the article, welcome to follow!