title: Clinical and biodiscovery implications of intra-specific venom variation in the medically important Southern Pacific Rattlesnake (Crotalus oreganus helleri)
design: Parameter settings seen for:  Sanger data (also common parameters), 454 data     Used parameter settings:    General (-GE):        Project name in (proin)                     : mira        Project name out (proout)                   : mira        Number of threads (not)                     : 2        Automatic memory management (amm)           : yes            Keep percent memory free (kpmf)         : 15            Max. process size (mps)                 : 0        EST SNP pipeline step (esps)                : 0        Use template information (uti)              :  [san]  yes                                                       [454]  yes            Template insert size minimum (tismin)   :  [san]  -1                                                       [454]  -1            Template insert size maximum (tismax)   :  [san]  -1                                                       [454]  -1            Template partner build direction (tpbd) :  [san]  -1                                                       [454]  -1        Colour reads by hash frequency (crhf)       : no       Load reads options (-LR):        Load sequence data (lsd)                    :  [san]  no                                                       [454]  yes            File type (ft)                          :  [san]  fasta                                                       [454]  fastq            External quality (eq)                   : from SCF (scf)                Ext. qual. override (eqo)           : no                Discard reads on e.q. error (droeqe): no            Solexa scores in qual file (ssiqf)      : no            FASTQ qual offset (fqqo)                :  [san]  0                                                       [454]  0           Wants quality file (wqf)                    :  [san]  yes                                                       [454]  yes           Read naming scheme (rns)                    :  [san] Sanger Institute (sanger)                                                       [454] forward/reverse (fr)           Merge with XML trace info (mxti)            :  [san]  no                                                       [454]  yes           Filecheck only (fo)                         : no       Assembly options (-AS):        Number of passes (nop)                      : 5            Skim each pass (sep)                    : yes        Maximum number of RMB break loops (rbl)     : 3        Maximum contigs per pass (mcpp)             : 0           Minimum read length (mrl)                   :  [san]  80                                                       [454]  40        Minimum reads per contig (mrpc)             :  [san]  2                                                       [454]  1        Base default quality (bdq)                  :  [san]  10                                                       [454]  10        Enforce presence of qualities (epoq)        :  [san]  yes                                                       [454]  yes           Automatic repeat detection (ard)            : no            Coverage threshold (ardct)              :  [san]  2                                                       [454]  2            Minimum length (ardml)                  :  [san]  400                                                       [454]  200            Grace length (ardgl)                    :  [san]  40                                                       [454]  20            Use uniform read distribution (urd)     : no              Start in pass (urdsip)                : 4              Cutoff multiplier (urdcm)             :  [san]  1.5                                                       [454]  1.5        Keep long repeats separated (klrs)          : no           Spoiler detection (sd)                      : no            Last pass only (sdlpo)                  : yes           Use genomic pathfinder (ugpf)               : no           Use emergency search stop (uess)            : yes            ESS partner depth (esspd)               : 500        Use emergency blacklist (uebl)              : yes        Use max. contig build time (umcbt)          : yes            Build time in seconds (bts)             : 3600       Strain and backbone options (-SB):        Load straindata (lsd)                       : no        Assign default strain (ads)                 :  [san]  no                                                       [454]  no            Default strain name (dsn)               :  [san]  StrainX                                                       [454]  StrainX        Load backbone (lb)                          : no            Start backbone usage in pass (sbuip)    : 3            Backbone file type (bft)                : fasta            Backbone base quality (bbq)             : 30            Backbone strain name (bsn)              : ReferenceStrain                Force for all (bsnffa)              : no            Backbone rail from strain (brfs)        :             Backbone rail length (brl)              : 0            Backbone rail overlap (bro)             : 0            Also build new contigs (abnc)           : yes       Dataprocessing options (-DP):        Use read extensions (ure)                   :  [san]  yes                                                       [454]  no            Read extension window length (rewl)     :  [san]  30                                                       [454]  15            Read extension w. maxerrors (rewme)     :  [san]  2                                                       [454]  2            First extension in pass (feip)          :  [san]  0                                                       [454]  0            Last extension in pass (leip)           :  [san]  0                                                       [454]  0       Clipping options (-CL):        Merge with SSAHA2/SMALT vector screen (msvs):  [san]  no                                                       [454]  no            Gap size (msvsgs)                       :  [san]  10                                                       [454]  8            Max front gap (msvsmfg)                 :  [san]  60                                                       [454]  8            Max end gap (msvsmeg)                   :  [san]  120                                                       [454]  12            Strict front clip (msvssfc)             :  [san]  0                                                       [454]  0            Strict end clip (msvssec)               :  [san]  0                                                       [454]  0        Possible vector leftover clip (pvlc)        :  [san]  yes                                                       [454]  no            maximum len allowed (pvcmla)            :  [san]  18                                                       [454]  18        Min qual. threshold for entire read (mqtfer):  [san]  0                                                       [454]  0            Number of bases (mqtfernob)             :  [san]  0                                                       [454]  0        Quality clip (qc)                           :  [san]  no                                                       [454]  no            Minimum quality (qcmq)                  :  [san]  20                                                       [454]  20            Window length (qcwl)                    :  [san]  30                                                       [454]  30        Bad stretch quality clip (bsqc)             :  [san]  yes                                                       [454]  no            Minimum quality (bsqcmq)                :  [san]  20                                                       [454]  5            Window length (bsqcwl)                  :  [san]  30                                                       [454]  20        Masked bases clip (mbc)                     :  [san]  yes                                                       [454]  yes            Gap size (mbcgs)                        :  [san]  20                                                       [454]  5            Max front gap (mbcmfg)                  :  [san]  40                                                       [454]  12            Max end gap (mbcmeg)                    :  [san]  60                                                       [454]  12        Lower case clip (lcc)                       :  [san]  no                                                       [454]  yes        Clip poly A/T at ends (cpat)                :  [san]  no                                                       [454]  yes            Keep poly-a signal (cpkps)              :  [san]  no                                                       [454]  no            Minimum signal length (cpmsl)           :  [san]  12                                                       [454]  12            Max errors allowed (cpmea)              :  [san]  1                                                       [454]  1            Max gap from ends (cpmgfe)              :  [san]  9                                                       [454]  20000        Clip 3 prime polybase (c3pp)                :  [san]  no                                                       [454]  no            Minimum signal length (c3ppmsl)         :  [san]  12                                                       [454]  12            Max errors allowed (c3ppmea)            :  [san]  2                                                       [454]  2            Max gap from ends (c3ppmgfe)            :  [san]  9                                                       [454]  9        Clip known adaptors right (ckar)            :  [san]  no                                                       [454]  yes        Ensure minimum left clip (emlc)             :  [san]  yes                                                       [454]  no            Minimum left clip req. (mlcr)           :  [san]  25                                                       [454]  4            Set minimum left clip to (smlc)         :  [san]  30                                                       [454]  4        Ensure minimum right clip (emrc)            :  [san]  no                                                       [454]  no            Minimum right clip req. (mrcr)          :  [san]  10                                                       [454]  10            Set minimum right clip to (smrc)        :  [san]  20                                                       [454]  15           Apply SKIM chimera detection clip (ascdc)   : no        Apply SKIM junk detection clip (asjdc)      : no           Propose end clips (pec)                     : no            Bases per hash (pecbph)                 : 17            Handle Solexa GGCxG problem (pechsgp)   : yes           Clip bad solexa ends (cbse)                 : yes       Parameters for SKIM algorithm (-SK):        Number of threads (not)                     : 2           Also compute reverse complements (acrc)     : yes        Bases per hash (bph)                        : 21        Hash save stepping (hss)                    : 1        Percent required (pr)                       :  [san]  70                                                       [454]  80           Max hits per read (mhpr)                    : 30        Max megahub ratio (mmhr)                    : 0           SW check on backbones (swcob)               : no           Freq. est. min normal (fenn)                : 0.4        Freq. est. max normal (fexn)                : 1.6        Freq. est. repeat (fer)                     : 1.9        Freq. est. heavy repeat (fehr)              : 8        Freq. est. crazy (fecr)                     : 20        Mask nasty repeats (mnr)                    : yes            Nasty repeat ratio (nrr)                : 100        Repeat level in info file (rliif)           : 6           Max hashes in memory (mhim)                 : 15000000        MemCap: hit reduction (mchr)                : 2048       Pathfinder options (-PF):        Use quick rule (uqr)                        :  [san]  yes                                                       [454]  yes            Quick rule min len 1 (qrml1)            :  [san]  200                                                       [454]  80            Quick rule min sim 1 (qrms1)            :  [san]  90                                                       [454]  90            Quick rule min len 2 (qrml2)            :  [san]  100                                                       [454]  60            Quick rule min sim 2 (qrms2)            :  [san]  95                                                       [454]  95        Backbone quick overlap min len (bqoml)      :  [san]  150                                                       [454]  80        Max. start cache fill time (mscft)          : 5       Align parameters for Smith-Waterman align (-AL):        Bandwidth in percent (bip)             :  [san]  20                                                  [454]  20        Bandwidth max (bmax)                   :  [san]  130                                                  [454]  80        Bandwidth min (bmin)                   :  [san]  25                                                  [454]  20        Minimum score (ms)                     :  [san]  30                                                  [454]  15        Minimum overlap (mo)                   :  [san]  17                                                  [454]  20        Minimum relative score in % (mrs)      :  [san]  70                                                  [454]  80        Solexa_hack_max_errors (shme)          :  [san]  0                                                  [454]  0        Extra gap penalty (egp)                :  [san]  no                                                  [454]  yes            extra gap penalty level (egpl)     :  [san] low                                                  [454] reject_codongaps            Max. egp in percent (megpp)        :  [san]  100                                                  [454]  100       Contig parameters (-CO):        Name prefix (np)                                         : mira        Reject on drop in relative alignment score in % (rodirs) :  [san]  25                                                                    [454]  15        Mark repeats (mr)                                        : yes            Only in result (mroir)                               : no            Assume SNP instead of repeats (asir)                 : no            Minimum reads per group needed for tagging (mrpg)    :  [san]  2                                                                    [454]  4            Minimum neighbour quality needed for tagging (mnq)   :  [san]  20                                                                    [454]  20            Minimum Group Quality needed for RMB Tagging (mgqrt) :  [san]  30                                                                   [454]  25            End-read Marking Exclusion Area in bases (emea)      :  [san]  25                                                                    [454]  10                Set to 1 on clipping PEC (emeas1clpec)           : yes            Also mark gap bases (amgb)                           :  [san]  yes                                                                    [454]  no                Also mark gap bases - even multicolumn (amgbemc) :  [san]  yes                                                                    [454]  yes                Also mark gap bases - need both strands (amgbnbs):  [san]  yes                                                                    [454]  yes        Force non-IUPAC consensus per sequencing type (fnicpst)  :  [san]  no                                                                    [454]  no        Merge short reads (msr)                                  :  [san]  no                                                                    [454]  no            Keep ends unmerged (msrkeu)                          :  [san]  -1                                                                    [454]  -1        Gap override ratio (gor)                                 :  [san]  66                                                                    [454]  66       Edit options (-ED):        Automatic contig editing (ace)              :  [san]  no                                                       [454]  yes       Sanger only:        Strict editing mode (sem)                   : no        Confirmation threshold in percent (ct)      : 50       Misc (-MI):        Stop on NFS (sonfs)                         : yes        Extended log (el)                           : no        Large contig size (lcs)                     : 500        Large contig size for stats(lcs4s)          : 1000        Stop on max read name length (somrnl)       : 40       Directories (-DI):        Working directory                 :         When loading EXP files            :         When loading SCF files            :         Top directory for writing files   : mira_assembly        For writing result files          : mira_assembly/mira_d_results        For writing result info files     : mira_assembly/mira_d_info        For writing tmp files             : /tmp//mira_d_tmp        Tmp redirected to (trt)           : /tmp/        For writing checkpoint files      : mira_assembly/mira_d_chkpt       File names (-FN):        When loading sequences from FASTA            :  [san]  mira_in.sanger.fasta                                                        [454]  mira_in.454.fasta        When loading qualities from FASTA quality    :  [san]  mira_in.sanger.fasta.qual                                                        [454]  mira_in.454.fasta.qual        When loading sequences from FASTQ            :  [san]  mira_in.sanger.fastq                                                        [454]  mira_in.454.fastq        When loading project from CAF                : mira_in.sanger.caf        When loading project from MAF (disabled)     : mira_in.sanger.maf        When loading EXP fofn                        : mira_in.sanger.fofn        When loading project from PHD                : mira_in.phd.1        When loading strain data                     : mira_straindata_in.txt        When loading XML trace info files            :  [san]  mira_traceinfo_in.sanger.xml                                                        [454]  mira_traceinfo_in.454.xml        When loading SSAHA2 vector screen results    : mira_ssaha2vectorscreen_in.txt        When loading SMALT vector screen results     : mira_smaltvectorscreen_in.txt           When loading backbone from MAF               : mira_backbone_in.maf        When loading backbone from CAF               : mira_backbone_in.caf        When loading backbone from GenBank           : mira_backbone_in.gbf        When loading backbone from GFF3              : mira_backbone_in.gff3        When loading backbone from FASTA             : mira_backbone_in.fasta          Output files (-OUTPUT/-OUT):        Save simple singlets in project (sssip)      :  [san]  no                                                        [454]  no        Save tagged singlets in project (stsip)      :  [san]  yes                                                        [454]  yes           Remove rollover tmps (rrot)                  : yes        Remove tmp directory (rtd)                   : no         Result files:        Saved as CAF                       (orc)     : yes        Saved as MAF                       (orm)     : yes        Saved as FASTA                     (orf)     : yes        Saved as GAP4 (directed assembly)  (org)     : no        Saved as phrap ACE                 (ora)     : yes        Saved as GFF3                     (org3)     : no        Saved as HTML                      (orh)     : no        Saved as Transposed Contig Summary (ors)     : yes        Saved as simple text format        (ort)     : no        Saved as wiggle                    (orw)     : no         Temporary result files:        Saved as CAF                       (otc)     : yes        Saved as MAF                       (otm)     : no        Saved as FASTA                     (otf)     : no        Saved as GAP4 (directed assembly)  (otg)     : no        Saved as phrap ACE                 (ota)     : no        Saved as HTML                      (oth)     : no        Saved as Transposed Contig Summary (ots)     : no        Saved as simple text format        (ott)     : no         Extended temporary result files:        Saved as CAF                      (oetc)     : no        Saved as FASTA                    (oetf)     : no        Saved as GAP4 (directed assembly) (oetg)     : no        Saved as phrap ACE                (oeta)     : no        Saved as HTML                     (oeth)     : no        Save also singlets               (oetas)     : no         Alignment output customisation:        TEXT characters per line (tcpl)              : 60        HTML characters per line (hcpl)              : 60        TEXT end gap fill character (tegfc)          :          HTML end gap fill character (hegfc)          :           File / directory output names:        CAF             : mira_out.caf        MAF             : mira_out.maf        FASTA           : mira_out.unpadded.fasta        FASTA quality   : mira_out.unpadded.fasta.qual        FASTA (padded)  : mira_out.padded.fasta        FASTA qual.(pad): mira_out.padded.fasta.qual        GAP4 (directory): mira_out.gap4da        ACE             : mira_out.ace        HTML            : mira_out.html        Simple text     : mira_out.txt        TCS overview    : mira_out.tcs        Wiggle          : mira_out.wig
library_name: Crotalus oreganus helleri (Catalina Island)