LSTrAP

installation

dependency

Required Tools

• Bowtie2
• TopHat
• HISAT2
• Samtools
• SRAtools
• HTSeq + all dependencies (including PySam)
• Python 3.5 + SciPy + Numpy
• MCL
• Trimmomatic

http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-centos_linux64.tar.gz

usage

ml Bowtie2
ml TopHat
ml HISAT2
ml SAMtools
ml SRAtools
ml HTSeq
ml MCL
ml Trimmomatic
java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.39.jar