1.3.1 Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., and Durbin R Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943] Assembly:Assemble_reads sam_xsede infile Input SAM file perl $sam_to_bam A1.sam sam_bam_command perl $sam_to_bam perl 'samtools_comet view -Shb A1.sam -o A1.bam &&' sort_bam_command perl $bam_sort perl 'samtools_comet sort A1.bam -o A1.bam.sorted &&' index_bam_command perl $bam_index perl 'samtools_comet index A1.bam.sorted' samtools_scheduler scheduler.conf perl "threads_per_process=12\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 output fasta output * runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.25 Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. Maximum Hours to Run must be less than 168 perl $runtime > 168.0 Maximum Hours to Run must be greater than 0.1 perl $runtime < 0.1 Please choose either SAM to BAM or BAM index perl !$bam_index && !$sam_to_bam Maximum Hours to Run must be greater than 0.1 perl $runtime < 0.1 The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 x $runtime cpu hours perl $runtime ne 0 perl "runhours=$value\\n" sam_to_bam Run Sam to BAM analysis (requires SAM input) 1 bam_sort Run BAM sort 1 inf_bam_sort BAM file to sort perl $bam_sort && !$sam_to_bam A1.bam This is the bam file. bam_index Run BAM index 1 This configuration requires BAM.sort file for input perl !$bam_sort && !$sam_to_bam inf_bam_index BAM file to index perl $bam_index && !$bam_sort && !$sam_to_bam A1.bam.sorted