Ubuntu Manpage: mirabait - a 'grep' like tool to select reads with kmers up to 256 bp

Provided by: mira-assembler_4.9.6-11_amd64

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 <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).

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:  <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

BUGS

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

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

AUTHOR

       Bastien Chevreux <bach@chevreux.org>

       This manual page was written by Bastien Chevreux <bach@chevreux.org>  but  can  be  freely
       used for any documentation purpose.

NAME

SYNOPSIS

DESCRIPTION

OPTIONS

Defining files types to load/save:

SEE ALSO

BUGS

AUTHOR