MIRACONVERT(1)

🦋 hey bestie, this is MIRACONVERT(1) 🦋

okay so real talk: you opened the user commands section of the manual and landed on miraconvert — and honestly? iconic. it's the little tool that takes your assembly and sequencing files and goes "and now you're a different format, slay." that's the whole vibe. converting file types. no cap. let's get into it 💅

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✨ NAME ✨

miraconvert — convert assembly and sequencing file types. that's it. that's the job. 🎀

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🌸 SYNOPSIS 🌸

look at this lil shape. it's giving "I take a lot of flags and I'm not sorry":

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

so basically: tell it where you're coming from, where you're going to (as many times as you want, queen), sprinkle in your flags, hand it an {infile} and an {outfile}, and optionally yell more <totype>s at the end. 🫶

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🔥 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 (and yes, you can mention -t multiple times, go off):
  • 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. not cute but there it is 💀

• -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.

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🧚 the contig-only switches (read the fine print, bestie)

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)

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🌈 EXAMPLES 🌈

here's the tea, copy-paste ready:

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? told you it was giving main character energy. 👑

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💜 SEE ALSO 💜

• mira(1), mirabait(1)

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

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💀 BUGS 💀

to report bugs or ask for features, please use the ticketing system at:

http://sourceforge.net/projects/mira-assembler/

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👑 AUTHOR 👑

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.

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and that's the whole page bestie!! ✨ this was miraconvert version 5.0.x, dated May 2016, straight out of the Debian universe. go convert something and make it everyone's problem 💅🦋🎀