--- name: "mirabait" section: "1" platform: "linux" package: "mira-assembler" version: "4.9.6-11" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/mirabait" --- # mirabait(1) a 'grep' like tool to select reads with kmers up to 256 bp ## NAME mirabait - a 'grep' like tool to select reads with kmers up to 256 bp ## SYNOPSIS mirabait \[options\] {-b baitfile \[-b ...\] \| **-B** file \| **-j** joblibrary} {-p file\_1 file\_2 \| **-P** file3}\* \[file4 ...\] ## DESCRIPTION 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. ## OPTIONS ### 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) - **-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**) - **-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 - **-I** Selects sequences that hit and do not hit bait (to different files) - **-r** No checking of reverse complement direction - **-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 - **-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 \ Has no effect if **-o**/-O is used and targets are not directories - **-o** \ 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** \ 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). ## Defining files types to load/save: 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: \::\. 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 ## SEE ALSO [mira(1)](/mira/1.md), [miraconvert(1)](/miraconvert/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 manual page was written by Bastien Chevreux \ but can be freely used for any documentation purpose.