mirabait − a ’grep’ like tool to select reads with kmers up to 256 bp
mirabait [options] {−b baitfile [−b ...] | −B file | −j joblibrary} {−p file_1 file_2 | −P file3}* [file4 ...]
mirabait selects reads from a read collection which are partly similar or equal to sequences defined as target baits. Similarity is defined by finding a user−adjustable number of common k−mers (sequences of k consecutive bases) which are the same in the bait sequences and the screened sequences to be selected, either in forward or forward/reverse complement direction. Adding a DUST−like repeat filter for repeats up 4 bases is optional.
When used on paired files, selects sequences where at least one mate matches.
Main options:
−b file
Load bait sequences from file (multiple −b allowed)
−B file
Load baits from kmer statistics file, not from sequence files. Only one −B allowed, cannot be combined with −b. (see −K for creating such a file)
−j job |
Set options for predefined job from supplied MIRA library Currently available jobs: |
rrna Bait rRNA sequences
−p file1 file2
Load paired sequences to search from file1 and file2 Files must contain same number of sequences, sequence names must be in same order. Multiple −p allowed, but must come before non−paired files.
−P file
Load paired sequences from file File must be interleaved: pairs must follow each other, non−pairs are not allowed. Multiple −p allowed, but must come before non−paired files.
−k int |
kmer length of bait in bases (<=256, default=31) |
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−n int |
If >0: minimum number of k−mer baits needed (default=1) If <=0: allowed number of missed kmers over sequence |
length
−d |
Do not use kmers with microrepeats (DUST−like, see also −D) |
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−D int |
Set length of microrepeats in kmers to discard from bait. |
− int > 0 microrepeat len in percentage of kmer length. E.g.: −k 17 −D 67 −−> 11.39 bases −−> 12 bases.
− int < 0 microrepeat len in bases.
− int != 0 implies −d, int=0 turns DUST filter off.
−i |
Selects sequences that do not hit bait |
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−I |
Selects sequences that hit and do not hit bait (to different files) |
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−r |
No checking of reverse complement direction |
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−t |
Number of threads to use (default=0 −> up to 4 CPU cores) |
Options for output definition:
Normally mirabait writes separate result files (named ’bait_match_*’ and ’bait_miss_*’) for each input to the current directory. For changing this behaviour and other relating to output, use these options:
−c |
No case change of sequence to denote bait hits |
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−l int |
length of a line (FASTA only, default 0=unlimited) |
−K file
Save kmer statistics to ’file’ (see also −B)
−N name
Change the prefix ’bait’ to <name> Has no effect if −o/−O is used and targets are not directories
−o <path>
Save sequences matching bait to path If path is a directory, write separate files into this directory. If not, combine all matching sequences from the input file(s) into a single file specified by the path.
−O <path>
Like −o, but for sequences not matching
Other options:
−T dir |
Use ’dir’ as directory for temporary files instead of current working directory. |
−m integer
Memory to use for computing kmer statistics
0..100 = use percentage of free system memory
>100 = amount of MiB to use (e.g. 16384 for 16 GiB)
Default 75 (75% of free system memory).
Normally mirabait recognises the file types according to the file extension (even when packed). In cases you need to force a certain file type because the file extension is non−standard, use the EMBOSS notation to force a type: <filetype>::<name_of_file>. E.g., to tell that "somefile.dat" is FASTQ, use: fastq::somefile.dat Recognised types are: caf, fasta, fastq, gbf, gbk, gbff, maf and phd.
MIRABAIT will write files in the same file type as the corresponding input files. Examples:
mirabait −b b.fasta file.fastq
mirabait −I −j rrna −p file_1.fastq file_2.fastq
mirabait −b b1.fasta −b b2.gbk file.fastq
mirabait −b fasta::baits.dat −p fastq::file_1.dat fastq::file_2.dat
mirabait −b b.fasta −p file_1.fastq file_2.fastq −P file3.fasta
file4.caf
mirabait −I −b b.fasta −p file_1.fastq file_2.fastq −P file3.fasta
file4.caf
mirabait −k 27 −n 10 −b b.fasta file.fastq
mirabait −b fasta::b.dat fastq::file.dat
mirabait −o /dev/shm/ −b b.fasta −p file_1.fastq file_2.fastq
mirabait −o /dev/shm/match −b b.fasta −p file_1.fastq file_2.fastq
mirabait −b human_genome.fasta −K HG_kmerstats.mhs.gz −p file1.fastq
file2.fastq
mirabait −B HG_kmerstats.mhs.gz −p file1.fastq file2.fastq
mirabait −d −B HG_kmerstats.mhs.gz −p file1.fastq file2.fastq
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 AT freelists DOT org
To report bugs or ask for features, please use the ticketing system at:
http://sourceforge.net/projects/mira-assembler/
Bastien Chevreux <bach AT chevreux DOT org>
This manual page was written by Bastien Chevreux <bach AT chevreux DOT org> but can be freely used for any documentation purpose.