.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.2.
.TH MIRABAIT "1" "May 2016" "mirabait 5.0.x" "User Commands"
.SH NAME
mirabait \- a 'grep' like tool to select reads with kmers up to 256 bp
.SH SYNOPSIS
mirabait [options]
{\-b baitfile [\-b ...] | \fB\-B\fR file | \fB\-j\fR joblibrary}
{\-p file_1 file_2 | \fB\-P\fR file3}* [file4 ...]
.SH 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.
.PP
When used on paired files, selects sequences where at least one mate matches.
.SH OPTIONS
.SS "Main options:"
.TP
\fB\-b\fR file
Load bait sequences from file
(multiple \fB\-b\fR allowed)
.TP
\fB\-B\fR file
Load baits from kmer statistics file, not from sequence files.
Only one \fB\-B\fR allowed, cannot be combined with \fB\-b\fR.
(see \fB\-K\fR for creating such a file)
.TP
\fB\-j\fR job
Set options for predefined job from supplied MIRA library
Currently available jobs:
.IP
rrna Bait rRNA sequences
.TP
\fB\-p\fR 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 \fB\-p\fR allowed, but must come before non\-paired
files.
.TP
\fB\-P\fR file
Load paired sequences from file
File must be interleaved: pairs must follow each other,
non\-pairs are not allowed.
Multiple \fB\-p\fR allowed, but must come before non\-paired
files.
.TP
\fB\-k\fR int
kmer length of bait in bases (<=256, default=31)
.TP
\fB\-n\fR int
If >0: minimum number of k\-mer baits needed (default=1)
If <=0: allowed number of missed kmers over sequence
.IP
length
.TP
\fB\-d\fR
Do not use kmers with microrepeats (DUST\-like, see also \fB\-D\fR)
.TP
\fB\-D\fR int
Set length of microrepeats in kmers to discard from bait.
.br
\- int > 0 microrepeat len in percentage of kmer length.
E.g.: \fB\-k\fR 17 \fB\-D\fR 67 \fB\-\-\fR> 11.39 bases \fB\-\-\fR> 12 bases.
.br
\- int < 0 microrepeat len in bases.
.br
\- int != 0 implies \fB\-d\fR, int=0 turns DUST filter off.
.TP
\fB\-i\fR
Selects sequences that do not hit bait
.TP
\fB\-I\fR
Selects sequences that hit and do not hit bait (to
different files)
.TP
\fB\-r\fR
No checking of reverse complement direction
.TP
\fB\-t\fR
Number of threads to use (default=0 \-> up to 4 CPU cores)
.SS
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:
.TP
\fB\-c\fR
No case change of sequence to denote bait hits
.TP
\fB\-l\fR int
length of a line (FASTA only, default 0=unlimited)
.TP
\fB\-K\fR file
Save kmer statistics to 'file' (see also \fB\-B\fR)
.TP
\fB\-N\fR name
Change the prefix 'bait' to <name>
Has no effect if \fB\-o\fR/\-O is used and targets are not
directories
.TP
\fB\-o\fR <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.
.TP
\fB\-O\fR <path>
Like \fB\-o\fR, but for sequences not matching
.SS "Other options:"
.TP
\fB\-T\fR dir
Use 'dir' as directory for temporary files instead of
current working directory.
.TP
\fB\-m\fR integer
Memory to use for computing kmer statistics
.br
0..100 = use percentage of free system memory
.br
>100 = amount of MiB to use (e.g. 16384 for 16 GiB)
.br
Default 75 (75% of free system memory).
.SH
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.
.PP
MIRABAIT will write files in the same file type as the corresponding input
files.
Examples:
.TP
mirabait \fB\-b\fR b.fasta file.fastq
.TP
mirabait \fB\-I\fR \fB\-j\fR rrna \fB\-p\fR file_1.fastq file_2.fastq
.TP
mirabait \fB\-b\fR b1.fasta \fB\-b\fR b2.gbk file.fastq
.TP
mirabait \fB\-b\fR fasta::baits.dat \fB\-p\fR fastq::file_1.dat fastq::file_2.dat
.TP
mirabait \fB\-b\fR b.fasta \fB\-p\fR file_1.fastq file_2.fastq \fB\-P\fR file3.fasta file4.caf
.TP
mirabait \fB\-I\fR \fB\-b\fR b.fasta \fB\-p\fR file_1.fastq file_2.fastq \fB\-P\fR file3.fasta file4.caf
.TP
mirabait \fB\-k\fR 27 \fB\-n\fR 10 \fB\-b\fR b.fasta file.fastq
.TP
mirabait \fB\-b\fR fasta::b.dat fastq::file.dat
.TP
mirabait \fB\-o\fR /dev/shm/ \fB\-b\fR b.fasta \fB\-p\fR file_1.fastq file_2.fastq
.TP
mirabait \fB\-o\fR \fI\,/dev/shm/match\/\fP \fB\-b\fR b.fasta \fB\-p\fR file_1.fastq file_2.fastq
.TP
mirabait \fB\-b\fR human_genome.fasta \fB\-K\fR HG_kmerstats.mhs.gz \fB\-p\fR file1.fastq file2.fastq
.TP
mirabait \fB\-B\fR HG_kmerstats.mhs.gz \fB\-p\fR file1.fastq file2.fastq
.TP
mirabait \fB\-d\fR \fB\-B\fR HG_kmerstats.mhs.gz \fB\-p\fR file1.fastq file2.fastq
.SH "SEE ALSO"
mira(1), miraconvert(1)
.PP
A more extensive documentation is provided in the MIRA manual available
online at
.IP
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html
.PP
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.
.PP
You can also subscribe one of the MIRA mailing lists at
.IP
http://www.chevreux.org/mira_mailinglists.html
.PP
After subscribing, mail general questions to the MIRA talk mailing list:
.IP
mira_talk@freelists.org
.SH BUGS
To report bugs or ask for features, please use the ticketing system at:
.IP
http://sourceforge.net/projects/mira-assembler/
.SH AUTHOR
Bastien Chevreux <bach@chevreux.org>
.PP
This manual page was written by Bastien Chevreux <bach@chevreux.org> but can
be freely used for any documentation purpose.