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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.

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
You can directly run bamlink from the folder. No extra setup is necessary.



    Prepare Data Description File

    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.

    Single command mode

    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)


    BAMLINK will produce a single .fasta file in FASTA format containing all scaffolds which have been used for scaffolding.