xenial (1) miraconvert.1.gz

Provided by: mira-assembler_4.9.5-5_amd64 bug

NAME

       miraconvert - convert assembly and sequencing file types

SYNOPSIS

       miraconvert  [-f  <fromtype>]  [-t  <totype>  [-t  <totype> ...]] [-aAChimMsuZ] [-cflnNoPqrtvxXyYz {...}]
       {infile} {outfile} [<totype> <totype> ...]

OPTIONS

       -f <fromtype>
              load this type of project files, where fromtype is:

              caf a complete assembly or single sequences from CAF

              maf a complete assembly or single sequences from CAF

              fasta sequences from a FASTA file

              fastq sequences from a FASTQ file

              gb[f|k|ff] sequences from a GenBank file

              phd sequences from a PHD file

              fofnexp sequences in EXP files from file of filenames

       -t <totype>
              write the sequences/assembly to this type (multiple mentions of -t are allowed):

              ace sequences or complete assembly to ACE

              caf sequences or complete assembly to CAF

              maf sequences or complete assembly to MAF

              sam complete assembly to SAM

              samnbb like above, but leaving out reference (backbones) in mapping assemblies

              gb[f|k|ff] sequences or consensus to GenBank

              gff3 consensus to GFF3

              wig assembly coverage info to wiggle file

              gcwig assembly gc content info to wiggle file

              fasta sequences or consensus to FASTA file (qualities to .qual)

              fastq sequences or consensus to FASTQ file

              exp sequences or complete assembly to EXP files in directories. Complete assemblies are suited for
              gap4 import as directed assembly.  Note: using caf2gap to import into gap4 is recommended though

              text complete assembly to text alignment (only when -f is caf, maf or gbf)

              html complete assembly to HTML (only when -f is caf, maf or gbf)

              tcs complete assembly to tcs

              hsnp surrounding of SNP tags (SROc, SAOc, SIOc) to HTML (only when -f is caf, maf or gbf)

              asnp analysis of SNP tags (only when -f is caf, maf or gbf)

              cstats contig statistics file like from MIRA (only when source contains contigs)

              crlist contig read list file like from MIRA (only when source contains contigs)

              maskedfasta  reads  where  sequencing  vector  is  masked out (with X) to FASTA file (qualities to
              .qual)

              scaf sequences or complete assembly to single sequences CAF

       -a     Append to target files instead of rewriting

       -A     Do not Adjust sequence case

              When reading formats which define clipping points,  and  saving  to  formats  which  do  not  have
              clipping  information,  miraconvert  normally  adjusts  the case of read sequences: lower case for
              clipped parts, upper case for unclipped parts of reads.  Use -A if you do not want this. See  also
              -C.

              Applies only to files/formats which do not contain contigs.

       -b     Blind data

              Replaces all bases in reads/contigs with a 'c'

       -C     Perform hard clip to reads

              When  reading  formats  which  define  clipping points, will save only the unclipped part into the
              result file.

              Applies only to files/formats which do not contain contigs.

       -d     Delete gap only columns

              When output is contigs: delete columns that are entirely gaps (like  after  having  deleted  reads
              during editing in gap4 or similar)

              When output is reads: delete gaps in reads

       -F     Filter read groups to different files

              Works  only  for  input  files  with readgroups (CAF/MAF) 3 (or 4) files generated: one or two for
              paired, one for unpaired and one for debris reads.

              Reads in paired file are interlaced by default, use -F twice to create separate files.

       -m     Make contigs (only for -t = caf or maf)

              Encase single reads as contig singlets into the CAF/MAF file.

       -n <filename>
              when given, selects only reads or contigs given by name in that file.

       -N <filename>
              like -n, but sorts output according to order given in file.

       -i     when -n is used, inverts the selection

       -o <quality>t
              FASTQ quality Offset (only for -f = 'fastq')

              Offset of quality values in FASTQ file. Default of 33 loads  Sanger/Phred  style  files,  using  0
              tries to automatically recognise.

       -P <string>
              String with MIRA parameters to be parsed

              Useful when setting parameters affecting consensus calling like -CO:mrpg etc.

              E.g.: -P "454_SETTINGS -CO:mrpg=3"

       -q <quality>
              Set  default  quality  for bases in file types without quality values. Furthermore, do not stop if
              expected quality files are missing (e.g. '.fasta')

       -R <name>
              Rename contigs/singlets/reads with given name string to which a counter is appended.

              Known bug: will create duplicate names if input contains contigs/singlets as well as  free  reads,
              i.e.  reads not in contigs nor singlets.

       -S <name>
              (name)Scheme for renaming reads, important for paired-ends. Only 'solexa' is currently supported.

       -T     When  converting  single  reads,  trim/clip  away  stretches  of  N and X and ends of reads. Note:
              remember to use -C to also perform a hard clip (e.g. with FASTA as output).

       -v     Print version number and exit

       -Y <integer>
              Yield. Max (clipped/padded) bases to convert.

              When used on reads: output will contain first reads of file where length of clipped  bases  totals
              at  least  -Y.   When  used  on contigs: output will contain first contigs of file where length of
              padded contigs totals at least -Y.

       The following switches work only when input (CAF or MAF) contains contigs. Beware: CAF and MAf  can  also
       contain just reads.

       -M     Do not extract contigs (or their consensus), but the sequence of the reads they are composed of.

       -r [cCqf]
              Recalculate consensus and / or consensus quality values and / or SNP feature tags.

              'c' recalc cons & cons qualities (with IUPAC)

              'C' recalc cons & cons qualities (forcing non-IUPAC)

              'q' recalc consensus qualities only

              'f' recalc SNP features

              Note: only the last of cCq is relevant, f works as a switch and can be combined with cQq (e.g. "-r
              C -r f")

              Note: if the CAF/MAF contains multiple strains, recalculation of cons & cons qualities is  forced,
              you can just influence whether IUPACs are used or not.

       -s     split output into multiple files instead of creating a single file

       -u     'fillUp strain genomes'

              Fill holes in the genome of one strain (N or @) with sequence from a consensus of other strains

              Takes  effect  only with -r and -t gbf or fasta/q in FASTA/Q: bases filled up are in lower case in
              GBF: bases filled up are in upper case

       -Q <integer>
              Defines minimum quality a consensus base of a strain must have, consensus bases below this will be
              'N' Default: 0

              Only used with -r, and -f is caf/maf and -t is (fasta or gbf)

       -V <integer>
              Defines  minimum  coverage  a consensus base of a strain must have, bases with coverage below this
              will be 'N' Default: 0

              Only used with -r, and -t is (fasta or gbf)

       -x <integer>
              Minimum contig or unclipped read length

              When loading, discard all contigs /  reads  with  a  length  less  than  this  value.  Default:  0
              (=switched off)

              Note: not applied to reads in contigs!

       -X <integer>
              Similar to -x but applies only to reads and then to the clipped length.

       -y <integer>
              Minimum  average  contig  coverage When loading, discard all contigs with an average coverage less
              than this value.  Default: 1

       -z <integer>
              Minimum number of reads in contig When loading, discard all contigs with a number  of  reads  less
              than this value.  Default: 0 (=switched off)

       -l <integer>
              when output as text or HTML: number of bases shown in one alignment line. Default: 60.

       -c <character>
              when output as text or HTML: character used to pad endgaps. Default: ' ' (blank)

EXAMPLES

              miraconvert source.maf dest.sam

              miraconvert source.caf dest.fasta wig ace

              miraconvert -x 2000 -y 10 source.caf dest.caf

              miraconvert -x 40 -C -F -F source.maf .fastq

              miraconvert: Missing infile and out-basename as arguments!

AUTHOR

       The program miraconvert was written by Bastien Chevreux <bach@chevreux.org>.

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.