Bamlink is a stand-alone scaffolding algorithm, which scaffolds contigs based on the direct alignment of paired-end reads. Bamlink has been tested on Illumina paired-end reads, mate-pair reads, 454 paired end reads, and BAC-end reads.
Bamlink was written in Perl by Xiangchao Gan.
The source code in Perl is available here . The current version is v0.1.0. Please send bug reports and comments to the authors.
Please download the software and decompress it.
You can directly run bamlink from the folder. No extra setup is necessary.
wget http://chi.mpipz.mpg.de/download/bamlink/bamlink-0.1.0.tar.gz tar -zxf bamlink-0.1.0.tar.gz cd bamlink-0.1.0
A typical project might involve the assembly of more than one library with different insert sizes. The description file tells how to interpret the input .bam files and do scaffolding in a hierarchical way. Please read the details carefully. A simple example example1 is provided. Users can revise accordingly.
bamlink.pl input.fasta <data_desctipiton_file>other options of Bamlink are as follows:
--config_file config file for the default parameters (default bamlinkdefault_config, optional) --out_tmpfolder path to the output folder (default: './') --out_tmpbasename Base name for all output files (default: 'blink') --out_seqfile output sequence file in fasta format (default: undefine) --mapqual Only use the read pairs with the mapping quality of both ends >= threshold (default: 20) --exclude Exclude contigs matching PATTERN --include Don't exclude contigs matching PATTERN --verbose Runs in verbose mode (-v 1=yes, -v 0=no, default: 0) --dotplot Make .dot file for visualisation of scaffolding (-p 1=yes, -p 0=no, default: 0)