--- name: "miraconvert" section: "1" platform: "linux" package: "mira-assembler" version: "4.9.6-11" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/miraconvert" --- # miraconvert(1) convert assembly and sequencing file types ## NAME miraconvert - convert assembly and sequencing file types ## SYNOPSIS **miraconvert** \[-f \\] \[-t \ \[-t \ ...\]\] \[-aAbCdhimMsuZ\] \[-cflnNoPqrtvxXyYz {...}\] {infile} {outfile} \[\ \ ...\] ## OPTIONS - **-f** *\* 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** *\* 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** \ when given, selects only reads or contigs given by name in that file. - **-N** \ like **-n**, but sorts output according to order given in file. - **-i** when **-n** is used, inverts the selection - **-o** \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 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** \ 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** \ 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)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** \ 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** \ 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** \ 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** \ 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** \ Similar to **-x** but applies only to reads and then to the clipped length. - **-y** \ Minimum average contig coverage When loading, discard all contigs with an average coverage less than this value. Default: 1 - **-z** \ 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** \ when output as text or HTML: number of bases shown in one alignment line. Default: 60. - **-c** \ 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 ## SEE ALSO [mira(1)](/mira/1.md), [mirabait(1)](/mirabait/1.md) A more extensive documentation is provided in the MIRA manual available online at - http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html On Debian, this can be installed with the mira-doc package and can then be found at /usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. On other systems, you may want to check in /usr/local/share/mira/doc or run "locate DefinitiveGuideToMIRA" to find it locally. You can also subscribe one of the MIRA mailing lists at - http://www.chevreux.org/mira\_mailinglists.html After subscribing, mail general questions to the MIRA talk mailing list: - mira\_talk@freelists.org ## BUGS To report bugs or ask for features, please use the ticketing system at: - http://sourceforge.net/projects/mira-assembler/ ## AUTHOR Bastien Chevreux \ This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.