GS De Novo Assembler and GS Reference Mapper Appendices

Option	Description	runAssembly	runMapping	runProject (Assembly)	runProject (Mapping)	gsAssembler	gsMapper
--help	Flag to display command usage	X	X	X	X	Help button	Help button
--version	Flag to display command version	X	X	X	X	About button	About button
-cdna	Flag for transcriptome projects	X (also newAssembly)	X (also newMapping)			Sequence Type dropdown menu	Sequence Type dropdown menu
-cpu #	Flag to specify number of CPUs to use for the computations. Default of ‘0’ means use all.	X	X	X	X	Parameters: Number of CPUs to use	Parameters: Number of CPUs to use
-minlen #	Flag to set the minimum length of reads used in the computations.	X	X	X	X	Parameters: Minimum read length	Parameters: Minimum read length
-qo	Flag to generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy.	X	X	X	X	Quick output toggle	Quick output toggle
-consed16	Flag to generate output compatible with versions of consed older than V17.0. (-consed is compatible with version 17.0)	X	X	X	X	ACE Format: consed16 selection	ACE Format: consed16 selection
-fe filename	Flag for exclude filter file to be specified.	X	X	X	X	Parameters: Exclude filter file	Parameters: Exclude filter file
-nofe	Flag to disable use of exclude filter file	X	X	X	X
-fi filename	Flag for include filter file to be specified.	X	X	X	X	Parameters: Include filter file	Parameters: Include filter file
-nofi	Flag to disable use of include filter file	X	X	X	X
-info	Flag to output to 454AlignmentInfo.tsv file.	X	X	X	X	Alignment info: Output small Selection	Alignment info: Output small Selection
-infoall	Flag to output to 454AlignmentInfo.tsv file including 0-coverage positions.	X	X	X	X	Alignment info: Output Selection	Alignment info: Output selection
-noinfo	Flag to suppress output of the 454AlignmentInfo.tsv file.	X	X	X	X	Alignment info: No output Selection	Alignment info: No output selection
-e #	Flag to specify expected depth of data, needed if depth >50, 0 resets to default	X	X	X	X	Parameters: Expected Depth field	Parameters: Expected Depth field
-m	Flag to keep sequence data in memory to speed up cpu time (requires large CPU memory)	X	X	X	X
-r	Flag to restart the computation			X	X	Parameters: Incremental De Novo assembler analysis toggle	Parameters: Incremental reference mapper analysis toggle
-o dir	Flag to open specified directory	X	X
-force	Flag required to overwrite an existing project directory	X	X
-p filedesc	Flag to specify SFF data in filedesc comes from Paired End sequencing	X (also addRun)	X (also addRun)			Treat reads as specified read type: dropdown menu	Treat reads as specified read type: dropdown menu
-mcf filedesc	Flag to specify non-default MID config file	X (also addRun)	X (also addRun)	X	X
-vs fastafile	Flag to specify a vector screening database FASTA file of read sequences that indicate contaminants. Read is screened if it matches completely, partial matches are not screened.	X	X	X	X	Parameters: Config Files; Screening database	Parameters: Config Files; Screening database
-novs	Flag to turn off a vector screening database used in an earlier part of the computation			X	X	Parameters: Config Files; Screening database (leave blank)	Parameters: Config Files; Screening database (leave blank)
-v fastafile -vt fastafile	Flag to specify a vector trimming database FASTA file for cloning vectors, primers, adaptors and other end sequences	X	X	X	X	Parameters: Config Files; Trimming database	Parameters: Config Files; Trimming database
-nov, -novt	Flag to turn off a vector trimming database FASTA file for cloning vectors, primers, adaptors and other end sequences specified in an earlier part of the computation			X	X	Parameters: Config Files; Trimming database (leave blank)	Parameters: Config Files; Trimming database (leave blank)
-notrim	Flag to turn off default quality and primer trimming of input reads	X	X	X	X		Parameters: Automatic Trimming toggle
-trim	Flag to turn on default quality and primer trimming of input reads			X	X		Parameters: Automatic Trimming toggle
-nor	Flag to turn off the automatic rescore function for read quality scores	X	X	X	X
-ud	Flag to treat each read separately, no grouping into duplicates	X	X	X	X
-ss	Flag to set the seed step parameter	X	X	X	X	Parameters: Seed step	Parameters: Seed step
-sl	Flag to set the seed length parameter	X	X	X	X	Parameters: Seed Length	Parameters: Seed Length
-sc	Flag to set the seed count parameter	X	X	X	X	Parameters: Seed Count	Parameters: Seed Count
-ml	Flag to set the minimum overlap length parameter (From the CLI, the value can be either a minimum length in bases or a percentage of read length. In the case of a percentage, simply include “%” immediately following the numeric value)	X	X	X	X	Parameters: Minimum Overlap Length	Parameters: Minimum Overlap Length
-mi	Flag to set the minimum overlap identity parameter	X	X	X	X	Parameters: Minimum Overlap Identity	Parameters: Minimum Overlap Identity
-ais	Flag to set the alignment identity score parameter	X	X	X	X	Parameters: Alignment Identity Score	Parameters: Alignment Identity Score
-ads	Flag to set the alignment difference score parameter	X	X	X	X	Parameters: Alignment Differenc Score	Parameters: Alignment Difference Score
-nrm	Flag to specify ‘no removal’ of meta data files which are needed for GUI viewing of data	X	X
-no	Flag to specify no output of most files. The output will include files associated with the creation of the multiple alignments, but will not include files or metrics involved with contig, consensus or variation information.	X	X	X	X	Include Consensus (not selected)	Include Consensus (not selected)
-nobig	Flag to skip output of large files; ACE Format files, 454PairAlign.txt, 454AlignmentInfo.tsv	X	X	X	X	Pairwise Alignment: None, ACE Format: No files Selections	Pairwise Alignment: None, Ace Format: No files Selections
-noace	Flag to specify no ace file generation	X	X	X	X	ACE Format: No files Selection	ACE Format: No files Selection
-ace	Flag to specify single ace file generation	X	X	X	X	ACE Format: Single ACE file Selection	Ace Format: Single Ace file Selection
-acedir	Flag to generate ace file subdirectory with an ace file for each contig output	X	X	X	X	ACE Format: Ace file per contig selection	ACE Format: Ace file per reference Selection
-consed	Flag to generate a consed file subdirectory and place all consed necessary file and folders within (consed V17.0)	X	X	X	X	ACE Format: Complete Consed Folder Selection	ACE Format: Complete Consed Folder Selection
-ar	Flag to output full raw read sequences in ace or consed folder	X	X	X	X	Ace read mode: raw selection	Ace read mode: raw selection
-at	Flag to output only trimmed sequence reads in ace or consed folder	X	X	X	X	Ace read mode: trimmed selection	Ace read mode: trimmed selection
-ad	Flag to use default to output reads in ACE or consed folder			X (trimmed)	X (raw)	Ace read mode: default (trimmed) selection	Ace read mode: default (raw) selection
-pair	Flag to output pairwise overlaps in txt file	X	X	X [also -p]	X [also -p]	Pairwise Alignment: Simple Selection	Pairwise Alignment: Simple Selection
-pairt	Flag to output pairwise overlaps in tab delim file	X	X	X [also -pt]	X [also -pt]	Pairwise Alignment: Tabbed selection	Pairwise Alignment: Tabbed selection
-tr	Flag to output 454TrimmedReads.fna & 454TrimmedReads.qual.	X	X	X	X	Parameter: Output trimmed reads	Parameter: Output trimmed reads
-a #	Flag to specify minimum length for contig reported in 454AllContif.fna. Default =100 For cDNA assembly, this value is set to 0 and can’t be changed	X	X	X	X	All contig threshold	All contig threshold
-l #	Flag to set the minimum length for contig to appear in 454LargeContigs.fna, default=500	X	X	X	X	Large contig threshold	Large contig threshold
-siom	Flag to invoke serial I/O and specify the size of the memory footprint to be used. Takes a numeric argument (in GB) from 1 – 1000.	X	X
-siod	Flag to invoke an alternate implementation of serial I/O that minimizes the disk space requirement.	X	X
-nosio	Flag to turn of –sio, -siom or –siod. Required to turn off serial I/O between consecutive runs of the same project.	X	X

Table 4: Mapping and Assembly options