# MITObim 1.9.1


## MITObim - mitochondrial baiting and iterative mapping

The pipeline was originally developed for Illumina data, but thanks to the
versatility of the MIRA assembler, MITObim supports in principle also data from
the Iontorrent, 454 and PacBio sequencing platforms.

Location and version:

```console
$ which MITObim.pl
/local/cluster/bin/MITObim.pl
$ MITObim.pl --version

MITObim - mitochondrial baiting and iterative mapping

version 1.9.1
```

help message:

```console
$ MITObim.pl --help

MITObim - mitochondrial baiting and iterative mapping

version 1.9.1


usage: ./MITObim.pl <parameters>

parameters:
		-start <int>		iteration to start with (default=0, when using '-quick' reference)
		-end <int>		iteration to end with (default=startiteration, i.e. if not specified otherwise stop after 1 iteration)
		-sample <string>	sampleID (please don't use '.' in the sampleID). If resuming, the sampleID needs to be identical to that of the previous iteration / MIRA assembly.
		-ref <string>		referenceID. If resuming, use the same as in previous iteration/initial MIRA assembly.
		-readpool <FILE>	readpool in fastq format (*.gz is also allowed). read pairs need to be interleaved for full functionality of the '-pair' option below.
                -quick <FILE>           reference sequence to be used as bait in fasta format
                -maf <FILE>             extracts reference from maf file created by previous MITObim iteration/MIRA assembly (resume)

optional:
		--kbait <int>		set kmer for baiting stringency (default: 31)
		--platform		specify sequencing platform (default: 'solexa'; other options: 'iontor', '454', 'pacbio')
		--denovo		runs MIRA in denovo mode
		--pair			extend readpool to contain full read pairs, even if only one member was baited (relies on /1 and /2 header convention for read pairs) (default: no).
		--verbose		show detailed output of MIRA modules (default: no)
		--split			split reference at positions with more than 5N (default: no)
		--help			shows this helpful information
		--clean                 retain only the last 2 iteration directories (default: no)
		--trimreads		trim data (default: no; we recommend to trim beforehand and feed MITObim with pre trimmed data)
		--trimoverhang		trim overhang up- and downstream of reference, i.e. don't extend the bait, just re-assemble (default: no)
		--mismatch <int>	number of allowed mismatches in mapping - only for illumina data (default: 15% of avg. read length)
		--min_cov <int>		minimum average coverage of contigs to be retained (default: 0 - off)
		--min_len <int>		minimum length of contig to be retained as backbone (default: 0 - off)
		--mirapath <string>     full path to MIRA binaries (only needed if MIRA is not in PATH)
		--redirect_tmp		redirect temporary output to this location (useful in case you are running MITObim on an NFS mount)
		--NFS_warn_only		allow MIRA to run on NFS mount without aborting -  warn only (expert option - see MIRA documentation 'check_nfs')
		--version		display MITObim version

examples:
		./MITObim.pl -start 1 -end 5 -sample StrainX -ref reference-mt -readpool illumina_readpool.fastq -maf initial_assembly.maf
		./MITObim.pl -end 10 -quick reference.fasta -sample StrainY -ref reference-mt -readpool illumina_readpool.fastq
```

software ref: <https://github.com/chrishah/MITObim>  
research ref: <https://doi.org/10.1093/nar/gkt371>