SPAdes on ACCESS 3.15.5 SPAdes for de novo assembly Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Korobeynikov, A., Lapidus, A., Prjibelski, A. D., Pyshkin, A., Sirotkin, A., Sirotkin, Y., Stepanauskas, R., Clingenpeel, S. R., Woyke, T., McLean, J. S., Lasken, R., Tesler, G., Alekseyev, M. A., and Pevzner, P. A. Bankevich, A., Nurk, S., Antipov, D., et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19, 455-477 10.1089/cmb.2012.0021 de Novo Sequence Assembly spades_access invocation perl $more_memory == 32 perl "spades_3.15.5_expanse$which_spades -t 16" 1 invocationb perl $more_memory >= 64 perl "spades_3.15.5_expanse$which_spades -t 32" 1 spades_scheduler scheduler.conf perl $more_memory == 32 perl "cpus-per-task=16\\n" . "max_file_size=unlimited\\n". "ntasks-per-node=1\\n" . "node_exclusive=0\\n" . "mem=32G\\n" . "nodes=1\\n" spades_scheduler2 scheduler.conf perl $more_memory == 64 perl "node_exclusive=0\\n" . "max_file_size=unlimited\\n". "cpus-per-task=32\\n" . "ntasks-per-node=1\\n" . "mem=64G\\n" . "nodes=1\\n" spades_scheduler3 scheduler.conf perl $more_memory == 128 perl "cpus-per-task=32\\n" . "max_file_size=unlimited\\n". "ntasks-per-node=1\\n" . "node_exclusive=0\\n" . "mem=128G\\n" . "nodes=1\\n" spades_scheduler4 scheduler.conf perl $more_memory == 243 perl "cpus-per-task=32\\n" . "max_file_size=unlimited\\n". "ntasks-per-node=1\\n" . "node_exclusive=1\\n" . "mem=243G\\n" . "nodes=1\\n" spades_scheduler5 scheduler.conf perl $more_memory == 512 perl "ChargeFactor=1.0\\n" . "max_file_size=unlimited\\n". "nodes=1\\n" . "large_data=1\\n" . "mem=500G\\n" . "node_exclusive=0\\n" . "cpus-per-task=32\\n" inputfile1_fastq inputfastq_1.fq.gz inputfile1S perl $specify_readtype eq "-s" perl "--s 1 inputfastq_1.fq.gz" 2 inputfile1_2 perl $specify_readtype ne "-s" perl "$specify_readtype$specify_inputtype 1 inputfastq_1.fq.gz" 2 runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 12 Estimate tLhe maximum time your job will need to run. We recommend testing 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 for a large memory node is 48 hours perl $runtime > 48.0 && $more_memory == 512 For high memory jobs, the run hours request must be greater than 6, but you will only be charged for the time your run actually uses perl $runtime <= 6 && $more_memory == 512 Maximum Hours to Run must be greater than 0.1 perl $runtime < 0.1 The job will run on 16 processors as configured. If it runs for the entire configured time, it will consume 16 x $runtime cpu hours perl $more_memory == 32 The job will run on 32 processors as configured. If it runs for the entire configured time, it will consume 32 x $runtime cpu hours perl $more_memory == 64 The job will run on 64 processors as configured. If it runs for the entire configured time, it will consume 64 x $runtime cpu hours perl $more_memory == 128 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $more_memory == 243 The job will run on 256 processors as configured. If it runs for the entire configured time, it will consume 256 x $runtime cpu hours perl $more_memory == 512 perl "runhours=$value\\n" which_spades Which spades version?: .gcc10.2.0 .gcc9.2.0 specify_readtype My read files are: --s --pe --hqmp Please select your read type perl !defined $specify_readtype specify_inputtype My first input file is: 80 -12 -1 -m inputfastq2r Select a reverse read file for Library 1 (gzipped) perl $specify_inputtype eq "-1" perl "$specify_readtype-2 1 inputfastq_R2_1.fq.gz" inputfastq_R2_1.fq.gz 3 Please select the reverse read file for Library 1 perl $specify_inputtype eq "-1" && !defined $inputfastq2r 13 pe_singlereads I have unpaired reads to go with my paired end read files (gzipped) perl $specify_inputtype eq "-1" || $specify_inputtype eq "-12" inputfastq1_singlepereads Select the file with unpaired fastq reads for PE Library 1 (gzipped) perl $specify_readtype eq "--pe" && $pe_singlereads perl "--pe1-s inputfastq_S1.fq.gz" inputfastq_S1.fq.gz 12 Advisory only: You did not choose a fastq single read file for paired end library 1; if you dont need one just click through. perl $specify_readtype ne "--s" && $pe_singlereads && !defined $inputfastq1_singlepereads 13 specify_librarynumber How many read libraries do you require? 1 2 3 4 5 6 7 8 9 name_spadesoutputdir Name for the spades output directory perl "-o spades_$name_spadesoutputdir" output 30 more_memory Please specify your memory requirement (in GB) 32 64 128 243 512 32 specify_datatype Specify your data type perl $specify_pipelineopt ne "--only-error-correction" --isolate --sc --meta perl defined $specify_datatype ? "$value":"" 31 Please specify the kind of data you are using (High coverage/single cell/metagenomic) perl !defined $specify_datatype && $specify_pipelineopt ne "--only-error-correction" specify_spadesmode Specify a specialized SPAdes mode --bio --corona --rna perl defined $specify_spadesmode ? "$value":"" 33 specify_spadespipeline Specify a specialized SPAdes pipeline --plasmid --metaviral --metaplasmid perl defined $specify_spadespipeline ? "$value":"" 35 Sorry, --plasmid cannot be used with single cell mode (--sc) perl $specify_spadespipeline eq "--plasmid" && $specify_datatype eq "--sc" Sorry, --metaplasmid cannot be used with single cell mode (--sc) perl $specify_spadespipeline eq "--metaplasmid" && $specify_datatype eq "--sc" specify_datasource Specify a specialized data source --rnaviral --iontorrent perl defined $specify_datasource ? "$value":"" 36 The --rnaviral option cannot be used with the --careful option perl $specify_datasource eq "--rnaviral" && $specify_pipelineopt2 The --rnaviral option cannot be used with the - -only-error-correction option perl $specify_datasource eq "--rnaviral" && $specify_pipelineopt eq "--only-error-correction" select_perlibs Interleaved Paired End Read Files (if you require more than one Library) inputfastq22 Select file for fastq read library 2 (interleaved; gzipped) inputfastq_2.fq.gz perl $specify_inputtype == "-12" && $specify_librarynumber > 1 && $specify_readtype ne "--s" perl "$specify_readtype$specify_inputtype 2 inputfastq_2.fq.gz" Please select the second paired end interleaved reads library perl $specify_inputtype == "-12" && $specify_librarynumber > 1 && $specify_readtype ne "--s" && !defined $inputfastq22 5 inputfastq23 Select file for fastq read library 3 (interleaved; gzipped) inputfastq_3.fq.gz perl $specify_inputtype == "-12" && $specify_librarynumber > 2 && $specify_readtype ne "--s" perl "$specify_readtype$specify_inputtype 3 inputfastq_3.fq.gz" Please select the third paired end interleaved only reads library perl $specify_inputtype == "-12" && $specify_librarynumber > 2 && $specify_readtype ne "--s" && !defined $inputfastq23 6 inputfastq24 Select file for fastq read library 4 (interleaved; gzipped) inputfastq_4.fq.gz perl $specify_inputtype == "-12" && $specify_librarynumber > 3 && $specify_readtype ne "--s" perl "$specify_readtype$specify_inputtype 4 inputfastq_4.fq.gz" Please select the fourth paired end interleaved reads library perl $specify_inputtype == "-12" && $specify_librarynumber > 3 && $specify_readtype ne "--s" && !defined $inputfastq24 7 inputfastq25 Select file for fastq read library 5 (interleaved; gzipped) inputfastq_5.fq.gz perl $specify_inputtype == "-12" && $specify_librarynumber > 4 && $specify_readtype ne "--s" perl "$specify_readtype$specify_inputtype 5 inputfastq_5.fq.gz" Please select the fifth paired end interleaved reads library perl $specify_inputtype == "-12" && $specify_librarynumber > 4 && $specify_readtype ne "--s" && !defined $inputfastq25 8 inputfastq26 Select file for fastq read library 6 (interleaved; gzipped) inputfastq_6.fq.gz perl $specify_inputtype == "-12" && $specify_librarynumber > 5 && $specify_readtype ne "--s" perl "$specify_readtype$specify_inputtype 6 inputfastq_6.fq.gz" Please select the sixth paired end interleaved reads library perl $specify_inputtype == "-12" && $specify_librarynumber > 5 && $specify_readtype ne "--s" && !defined $inputfastq26 9 inputfastq27 Select file for fastq read library 7 (interleaved; gzipped) inputfastq_7.fq.gz perl $specify_inputtype == "-12" && $specify_librarynumber > 6 && $specify_readtype ne "--s" perl "$specify_readtype$specify_inputtype 7 inputfastq_7.fq.gz" Please select the seventh paired end interleaved reads library perl $specify_inputtype == "-12" && $specify_librarynumber > 6 && $specify_readtype ne "--s" && !defined $inputfastq27 10 inputfastq28 Select file for fastq read library 8 (interleaved; gzipped) inputfastq_8.fq.gz perl $specify_inputtype == "-12" && $specify_librarynumber > 7 && $specify_readtype ne "--s" perl "$specify_readtype$specify_inputtype 8 inputfastq_8.fq.gz" Please select the eighth paired end interleaved or forward only reads library perl $specify_inputtype == "-12" && $specify_librarynumber > 7 && $specify_readtype ne "--s" && !defined $inputfastq28 11 inputfastq29 Select file for fastq read library 9 (interleaved; gzipped) inputfastq_9.fq.gz perl $specify_inputtype == "-12" && $specify_librarynumber > 8 && $specify_readtype ne "--s" perl "$specify_readtype$specify_inputtype 9 inputfastq_9.fq.gz" Please select the ninth paired end interleaved reads library perl $specify_inputtype == "-12" && $specify_librarynumber > 8 && $specify_readtype ne "--s" && !defined $inputfastq29 12 select_pefronlylibs Separate Forward and Reverse Paired End Read Files (if you require more than one Library) inputfastq22f Select file for fastq read library 2 (forward only reads; gzipped) inputfastq_R1_2.fq.gz perl $specify_librarynumber > 1 && $specify_inputtype == "-1" perl "$specify_readtype$specify_inputtype 2 inputfastq_R1_2.fq.gz" Please select the second paired end forward only reads library perl $specify_inputtype == "-1" && $specify_librarynumber > 1 && !defined $inputfastq22f 5 inputfastq22r Select file for fastq read library 2 (reverse only reads; gzipped) inputfastq_R2_2.fq.gz perl $specify_librarynumber > 1 && $specify_inputtype eq "-1" perl "$specify_readtype-2 2 inputfastq_R2_2.fq.gz" Please select the reverse read file for library 2 perl $specify_librarynumber > 1 && $specify_inputtype eq "-1" && !defined $inputfastq22r 6 inputfastq23f Select file for fastq read library 3 (forward only reads; gzipped) perl $specify_librarynumber > 2 && $specify_inputtype eq "-1" perl "$specify_readtype$specify_inputtype 3 inputfastq_R1_3.fq.gz" inputfastq_R1_3.fq.gz Please select the third paired end forward only reads library perl $specify_inputtype == "-1" && $specify_librarynumber > 2 && $specify_readtype ne "--s" && !defined $inputfastq23f 7 inputfastq23r Select file for fastq read library 3 (reverse only reads; gzipped) perl $specify_librarynumber > 2 && $specify_inputtype eq "-1" perl "$specify_readtype-2 3 inputfastq_R2_3.fq.gz" inputfastq_R2_3.fq.gz Please select the reverse read file for library 3 perl $specify_librarynumber > 2 && $specify_inputtype eq "-1" && !defined $inputfastq23r 8 inputfastq24f Select file for fastq read library 4 (forward only reads; gzipped) perl $specify_librarynumber > 3 && $specify_inputtype eq "-1" perl "$specify_readtype$specify_inputtype 4 inputfastq_R1_4.fq.gz" inputfastq_R1_4.fq.gz Please select the fourth paired end forward only reads library perl $specify_inputtype == "-1" && $specify_librarynumber > 3 && $specify_readtype ne "--s" && !defined $inputfastq24f 9 inputfastq24r Select file for fastq read library 4 (reverse only reads; gzipped) perl $specify_librarynumber > 3 && $specify_inputtype eq "-1" perl "$specify_readtype-2 4 inputfastq_R2_4.fq.gz" inputfastq_R2_4.fq.gz Please select the reverse read file for library 4 perl $specify_librarynumber > 3 && $specify_inputtype eq "-1" && !defined $inputfastq24r 10 inputfastq25f Select file for fastq read library 5 (forward only reads; gzipped) perl $specify_librarynumber > 4 && $specify_inputtype eq "-1" perl "$specify_readtype$specify_inputtype 5 inputfastq_R1_5.fq.gz" inputfastq_R1_5.fq.gz Please select the fifth paired end, forward only reads library file perl $specify_inputtype == "-1" && $specify_librarynumber > 4 && $specify_readtype ne "--s" && !defined $inputfastq25f 11 inputfastq25r Select file for fastq read library 5 (reverse only reads; gzipped) perl $specify_librarynumber > 4 && $specify_inputtype eq "-1" perl "$specify_readtype-2 5 inputfastq_R2_5.fq.gz" inputfastq_R2_5.fq.gz Please select the reverse read file for library 5 perl $specify_librarynumber > 4 && $specify_inputtype eq "-1" && !defined $inputfastq25r 12 inputfastq26f Select file for fastq read library 6 (forward only reads; gzipped) perl $specify_librarynumber > 5 && $specify_inputtype eq "-1" perl "$specify_readtype$specify_inputtype 6 inputfastq_R1_6.fq.gz" inputfastq_R1_6.fq.gz Please select the sixth paired end forward only reads library perl $specify_inputtype == "-1" && $specify_librarynumber > 5 && $specify_readtype ne "--s" && !defined $inputfastq26f 13 inputfastq26r Select file for fastq read library 6 (reverse only reads; gzipped) perl $specify_librarynumber > 5 && $specify_inputtype eq "-1" perl "$specify_readtype-2 6 inputfastq_R2_6.fq.gz" inputfastq_R2_6.fq.gz Please select the reverse reads file for library 6 perl $specify_librarynumber > 5 && $specify_inputtype eq "-1" && !defined $inputfastq26r 14 inputfastq27f Select file for fastq read library 7 (forward only reads; gzipped) perl $specify_librarynumber > 6 && $specify_inputtype eq "-1" perl "$specify_readtype$specify_inputtype 7 inputfastq_R1_7.fq.gz" inputfastq_R1_7.fq.gz Please select the seventh paired end forward only reads library perl $specify_inputtype == "-1" && $specify_librarynumber > 6 && $specify_readtype ne "--s" && !defined $inputfastq27f 15 inputfastq27r Select file for fastq read library 7 (reverse only reads; gzipped) perl $specify_librarynumber > 6 && $specify_inputtype eq "-1" perl "$specify_readtype-2 7 inputfastq_R2_7.fq.gz" inputfastq_R2_7.fq.gz Please select the reverse reads file for library 7 perl $specify_librarynumber > 6 && $specify_inputtype eq "-1" && !defined $inputfastq27r 16 inputfastq28f Select file for fastq read library 8 (forward only reads; gzipped) perl $specify_librarynumber > 7 && $specify_inputtype eq "-1" perl "$specify_readtype$specify_inputtype 8 inputfastq_R1_8.fq.gz" inputfastq_R1_8.fq.gz Please select the eighth paired end forward only reads library perl $specify_inputtype == "-1" && $specify_librarynumber > 7 && $specify_readtype ne "--s" && !defined $inputfastq28f 17 inputfastq28r Select file for fastq read library 8 (reverse only reads; gzipped) perl $specify_librarynumber > 7 && $specify_inputtype eq "-1" perl "$specify_readtype-2 8 inputfastq_R2_8.fq.gz" inputfastq_R2_8.fq.gz Please select the reverse reads file for library 8 perl $specify_librarynumber > 7 && $specify_inputtype eq "-1" && !defined $inputfastq28r 18 inputfastq29f Select file for fastq read library 9 (forward only reads; gzipped) perl $specify_librarynumber > 8 && $specify_inputtype eq "-1" perl "$specify_readtype$specify_inputtype 9 inputfastq_R1_9.fq.gz" inputfastq_R1_9.fq.gz Please select the ninth paired end forward only reads library perl $specify_inputtype == "-1" && $specify_librarynumber > 8 && $specify_readtype ne "--s" && !defined $inputfastq29f 19 inputfastq29r Select file for fastq read library 9 (reverse only reads; gzipped) perl $specify_librarynumber > 8 && $specify_inputtype eq "-1" perl "$specify_readtype-2 9 inputfastq_R2_9.fq.gz" inputfastq_R2_9.fq.gz Please select the reverse reads file for library 9 perl $specify_librarynumber > 8 && $specify_inputtype eq "-1" && !defined $inputfastq29r 20 select_singlelibspe Unpaired Paired End Sequence Files (for up to nine libraries; optional) inputfastq22srpe Select the fastq single read file for paired end library 2 (gzipped) inputfastq_sr2.fq.gz perl $specify_librarynumber > 1 && $specify_readtype ne "--s" perl "--pe-s 2 inputfastq_sr2.fq.gz" Advisory only: You did not choose a fastq single read file for paired end library 2; if you dont need one just click through. perl $specify_librarynumber > 1 && $specify_readtype ne "--s" && $pe_singlereads && !defined $inputfastq22srpe 5 inputfastq23srpe Select the fastq single read file for paired end library 3 (gzipped) inputfastq_sr3.fq.gz perl $specify_librarynumber > 2 && $specify_readtype ne "--s" perl "--pe-s 3 inputfastq_sr3.fq.gz" Advisory only: You did not choose a fastq single read file for paired end library 3; if you dont need one just click through. perl $specify_librarynumber > 2 && $specify_readtype ne "--s" && $pe_singlereads && !defined $inputfastq23srpe 6 inputfastq24srpe Select the fastq single read file for paired end library 4 (gzipped) inputfastq_4sr.fq.gz perl $specify_librarynumber > 3 && $specify_readtype ne "--s" perl "--pe-s 4 inputfastq_4sr.fq.gz" Advisory only: You did not choose a fastq single read file for paired end library 4; if you dont need one just click through. perl $specify_librarynumber > 3 && $specify_readtype ne "--s" && $pe_singlereads && !defined $inputfastq24srpe 8 inputfastq25srpe Select the fastq single read file for paired end library 5 (gzipped) perl $specify_librarynumber > 4 && $specify_readtype ne "--s" perl "--pe-s 5 inputfastq_5sr.fq.gz" inputfastq_5sr.fq.gz Advisory only: You did not choose a fastq single read file for paired end library 5; if you dont need one just click through. perl $specify_librarynumber > 4 && $specify_readtype ne "--s" && $pe_singlereads && !defined $inputfastq25srpe 9 inputfastq26srpe Select the fastq single read file for paired end library 6 (gzipped) inputfastq_6sr.fq.gz perl $specify_librarynumber > 5 && $specify_readtype ne "--s" perl "--pe-s 6 inputfastq_6sr.fq.gz" Advisory only: You did not choose a fastq single read file for paired end library 6; if you dont need one just click through. perl $specify_librarynumber > 5 && $specify_readtype ne "--s" && $pe_singlereads && !defined $inputfastq26srpe 10 inputfastq27srpe Select the fastq single read file for paired end library 7 (gzipped) inputfastq_7sr.fq.gz perl $specify_librarynumber > 6 && $specify_readtype ne "--s" perl "--pe-s 7 inputfastq_7sr.fq.gz" Advisory only: You did not choose a fastq single read file for paired end library 7; if you dont need one just click through. perl $specify_librarynumber > 6 && $specify_readtype ne "--s" && $pe_singlereads && !defined $inputfastq27srpe 11 inputfastq28srpe Select the fastq single read file for paired end library 8 (gzipped) inputfastq_8sr.fq.gz perl $specify_librarynumber > 7 && $specify_readtype ne "--s" perl "--pe-s 8 inputfastq_8sr.fq.gz" Advisory only: You did not choose a fastq single read file for paired end library 8; if you dont need one just click through. perl $specify_librarynumber > 7 && $specify_readtype ne "--s" && $pe_singlereads && !defined $inputfastq28srpe 12 inputfastq29srpe Select the fastq single read file for paired end library 9 (gzipped) inputfastq_8sr.fq.gz perl $specify_librarynumber > 8 && $specify_readtype ne "--s" perl "--pe-s 9 inputfastq_9sr.fq.gz" Advisory only: You did not choose a fastq single read file for paired end library 9; if you dont need one just click through. perl $specify_librarynumber > 8 && $specify_readtype ne "--s" && $pe_singlereads && !defined $inputfastq29srpe 13 select_singlelibs Single Read Files (up to 9 single read libraries) inputfastq22sr Select fastq single reads file for library 2 (gzipped) inputfastq_sr2.fq.gz perl $specify_librarynumber > 1 && $specify_inputtype eq "80" perl "--s2 inputfastq_sr2.fq.gz" Please select the single reads file for the second library perl $specify_librarynumber > 1 && $specify_inputtype eq "80" && !defined $inputfastq22sr 5 inputfastq23sr Select fastq single reads file for library 3 (gzipped) inputfastq_sr3.fq.gz perl $specify_librarynumber > 2 && $specify_inputtype eq "80" perl "--s3 inputfastq_sr3.fq.gz" Please select the single reads file for the third library perl $specify_librarynumber > 2 && $specify_inputtype eq "80" && !defined $inputfastq23sr 6 inputfastq24sr Select fastq single reads file for library 4 (gzipped) inputfastq_4sr.fq.gz perl $specify_librarynumber > 3 && $specify_inputtype eq "80" perl "--s4 inputfastq_4sr.fq.gz" Please select the single reads file for the fourth library perl $specify_librarynumber > 3 && $specify_inputtype eq "80" && !defined $inputfastq24sr 8 inputfastq25sr Select fastq single reads file for library 5 (gzipped) inputfastq_5sr.fq.gz perl $specify_librarynumber > 4 && $specify_inputtype eq "80" perl "--s5 inputfastq_5sr.fq.gz" Please select the single reads file for the fifth library perl $specify_librarynumber > 4 && $specify_inputtype eq "80" && !defined $inputfastq25sr 9 inputfastq26sr Select fastq single reads file for library 6 (gzipped) inputfastq_6sr.fq.gz perl $specify_librarynumber > 5 && $specify_inputtype eq "80" perl "--s6 inputfastq_6sr.fq.gz" Please select the single reads file for the sixth library perl $specify_librarynumber > 5 && $specify_inputtype eq "80" && !defined $inputfastq26sr 10 inputfastq27sr Select fastq single reads file for library 7 (gzipped) inputfastq_7sr.fq.gz perl $specify_librarynumber > 6 && $specify_inputtype eq "80" perl "--s7 inputfastq_7sr.fq.gz" Please select the single reads file for the seventh library perl $specify_librarynumber > 6 && $specify_inputtype eq "80" && !defined $inputfastq27sr 11 inputfastq28sr Select fastq single reads file for library 8 (gzipped)) inputfastq_8sr.fq.gz perl $specify_librarynumber > 7 && $specify_inputtype eq "80" perl "--s8 inputfastq_8sr.fq.gz" Please select the single reads file for the eighth library perl $specify_librarynumber > 7 && $specify_inputtype eq "80" && !defined $inputfastq28sr 12 inputfastq29sr Select fastq single reads file for library 9 (gzipped) inputfastq_8sr.fq.gz perl $specify_librarynumber > 8 && $specify_inputtype eq "80" perl "--s9 inputfastq_9sr.fq.gz" Please select the single reads file for the ninth library perl $specify_librarynumber > 8 && $specify_inputtype eq "80" && !defined $inputfastq29sr 13 hybrid_options Hybrid Assembly Options specify_pacbio Specify a PacBio readfile perl defined $specify_pacbio ? "--pacbio pacbio.fq.gz":"" pacbio.fq.gz 37 specify_nanopore Specify a Nanopore readfile perl defined $specify_nanopore ? "--nanopore nanopore.fq.gz":"" nanopore.fq.gz 38 specify_sanger Specify a Sanger readfile perl defined $specify_sanger ? "--sanger sanger.fq.gz":"" sanger.fq.gz 39 specify_trusted Specify a Trusted Contig file perl defined $specify_trusted ? "--trusted trusted.fq.gz":"" trusted.fq.gz 40 specify_untrusted Specify an Untrusted Contig file perl defined $specify_untrusted ? "--untrusted-contigs trusted.fq.gz":"" untrusted.fq.gz 41 pipeline_options Pipeline Options specify_pipelineopt Specify the Pipeline to run --only-error-correction --only-assembler perl defined $specify_pipelineopt ? "$value":"" 42 specify_pipelineopt2 Minimize number of mismatches and short indels perl $specify_datatype eq "--sc" perl $specify_pipelineopt2 ? "--careful":"" The --careful option is only recommended for small genomes perl $specify_pipelineopt2 43 specify_pipelineopt3 Save all check-points (default=last) perl $specify_pipelineopt3 ? "--checkpoint all":"" 44 specify_pipelineopt5 Do not compress the corrected reads perl $specify_pipelineopt ne "--only-assembler" perl $specify_pipelineopt5 ? "--disable-gzip-output":"" 45 specify_pipelineopt6 Disable repeat resolution stage of assembling perl $specify_pipelineopt6 ? "--disable-rr":"" 46 advanced_options Advanced SPAdes Options specify_yaml File with dataset description in YAML format perl "--dataset $value" data_description.yaml 47 specify_kmer Specify the kmer values perl defined $specify_kmer ? "-k $value":"" 21,33,55,77,99,127 48 specify_covcutoff Specify the coverage cutoff value perl $specify_datatype ne "--meta" perl defined $specify_covcutoff ? "--cov-cutoff $value":"" 49 specify_phredoffset Specify the Phrad quality offset 33 64 perl defined $specify_phredoffset ? "--phred-offset $value":"" 50 all_outputfiles *