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    The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
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    fast_count_multi

    Extremely fast NGS read counter

    .../fast_count_multi num_threads gtf_file bam_file(s) > output Requires bamtools API library at run time, and c++0x for compile. git clone https://github.com/pezmaster31/bamtools cd bamtools mkdir build cd build cmake .. make export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path to/lib g++ -I bamtools/include/ -L bamtools/lib/ -o fast_count_multi fast_count_multi.cpp -lz -lbamtools -fpermissive -pthread -std=c++0x
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