Source/additional information: http://canu.readthedocs.io/en/latest/quick-start.html#quickstart ==================================================================================== Set up: echo $SCRATCH cd $SCRATCH mkdir NGS_assembly_Apr18 mkdir NGS_assembly_Apr18/Long_Reads mkdir NGS_assembly_Apr18/Long_Reads/PacBio_Assembly mkdir NGS_assembly_Apr18/Long_Reads/PacBio_Data cd NGS_assembly_Apr18/Long_Reads/PacBio_Data curl -L -o pacbio.fastq http://gembox.cbcb.umd.edu/mhap/raw/ecoli_p6_25x.filtered.fastq head -n 16 pacbio.fastq ==================================================================================== Running Canu on TAMU HPRC Ada System: https://hprc.tamu.edu/wiki/Ada:NGS:Genome_Assembly#Canu module spider Canu module load Canu/1.5-intel-2015B-Perl-5.20.0 ++++++++++++++++++++++++++++++++++++++++++ Running Canu: head -n4 pacbio.fastq cp /scratch/training/NGS_assembly/Scripts/Canu_All_PacBio.sh $SCRATCH/NGS_assembly_Apr18/Long_Reads/PacBio_Assembly cd $SCRATCH/NGS_assembly_Apr18/Long_Reads/PacBio_Assembly cat Canu_All_PacBio.sh bsub < Canu_All_PacBio.sh bjobs ++++++++++++++++++++++++++++++++++++++++++ - Getting N50 cd /path_to_unitig_folder/unitigging tgStoreDump -G *.gkpStore -T *.ctgStore 2 -sizes -s 4800000