NGS Assembly using Velveth and Velvetg velvet_pre_script3.pl $output $output.id $__new_file_path__ #if $reads.sspace.run_sspace == "yes" $reads.sspace.insert_variation $reads.sspace.pair_type #end if #if $reads.sspace.run_sspace == "no" void void #end if -s $kmin -e $kmax -k $optFuncKmer -f ' #for $i in $inputs ${i.file_format} ${i.read_type} ${i.input} #end for ' #if $contig_lgth.use_contig_lgth == "yes" -o ' -min_contig_lgth $contig_lgth.min_contig_lgth #end if #if $reads.paired == "yes": #if $contig_lgth.use_contig_lgth == "no" -o ' #end if #if int(str($reads.ins_length)) > 0: -ins_length $reads.ins_length #end if #if $reads.options.advanced == "yes": #if int(str($reads.options.ins_length_sd)) > 0: -ins_length_sd $reads.options.ins_length_sd #end if #if int(str($reads.options.ins_length2)) > 0: -ins_length2 $reads.options.ins_length2 #end if #if int(str($reads.options.ins_length2_sd)) > 0: -ins_length2_sd $reads.options.ins_length2_sd #end if #if int(str($reads.options.ins_length_long)) > 0: -ins_length_long $reads.options.ins_length_long #end if #if int(str($reads.options.ins_length_long_sd)) > 0: -ins_length_long_sd $reads.options.ins_length_long_sd #end if #if int(str($reads.options.max_branch_length)) > 0: -max_branch_length $reads.options.max_branch_length #end if #if int(str($reads.options.max_gap_count)) > 0: -max_gap_count $reads.options.max_gap_count #end if #if int(str($reads.options.min_pair_count)) > 0: -min_pair_count $reads.options.min_pair_count #end if #if int(str($reads.options.long_mult_cutoff)) > 0: -long_mult_cutoff $reads.options.long_mult_cutoff #end if $reads.options.scaffolding #end if #end if #if $contig_lgth.use_contig_lgth == "yes" or $reads.paired == "yes": ' #end if Total number of contigs (ncon) Total number of base pairs in contigs (tbp) Length of the longest contig (max) Number of large (>1kb) contigs (Lcon) Total number of base pairs in large contigs (Lbp) The N50 (n50) The N50 + the length of the longest contig (n50+max) fasta fastq short reads shortPaired reads short2 reads shortPaired2 reads long reads longPaired reads No Yes No Yes Use Defaults Set Advanced Option Values Do not scaffold velvet output Scaffold contigs using SSPACE Mate-paired reads Paired-end reads

XXXXXXXXXXXXXXX This tool performs a multiple sequence alignment of the specified data on the Bioinformatics Condor compute cluster, using the parallel MPI implementation of clustalW. .. class:: warningmark While this tool should be able to handle most sequence formats it is recommended that sequences are submitted in the FASTA format. ---- The length of time it takes to complete the alignment will depend on the number and length of sequences submitted, however it will be significantly faster than most desktop PCs. Example times: * 50 1Kb sequences in approximately 50 seconds * 200 1Kb sequences in approximately 2 minutes * 600 1Kb sequences in approximately 10 minutes * 900 0.5-1.7Kb sequences in approximately 40 minutes Please be patient. The alignment will complete eventually. .. class:: warningmark The compute cluster is a finite resource and it may be that your job is delayed by the presence of others that are already running. You may want to check the status of the cluster (**Cluster tools > check cluster status**) before running a sequence alignment. At least 10 unclaimed nodes are required to run an alignment. Alignments submitted insufficient resources are available will be queued for execution and will run as soon as 10 nodes are free.