Galaxy |

MITObim (version 1.9.1)

Reference:

If a FASTA sequence is given it will be used as bait (using the --quick option). If a MAF alignment is given the reference is extracted from the alignment (using the --maf option)

Reference ID:

If resuming, use the same as in previous iteration/initial MIRA assembly

Read pool:

Read pairs need to be interleaved for full functionality of the '-pair' option below

Sample ID:

If resuming, the sampleID needs to be identical to that of the previous iteration / MIRA assembly

Iteration to start with:

Defaults to 0 when using '--quick' reference

Iteration to end with:

Default=startiteration, i.e. if not specified otherwise stop after 1 iteration

kmer for baiting stringency:

Sequencing platform:

Run MIRA in denovo mode:

Extend readpool to contain full read pairs, even if only one member was baited:

Relies on /1 and /2 header convention for read pairs

Split reference at positions with more than 5N:

Trim data:

It is recommended to trim beforehand and feed MITObim with pre trimmed data

Trim overhang:

up- and downstream of reference. That is don't extend the bait

Number of allowed mismatches in mapping:

Only for illumina data (default: 15% of avg. read length)

Minimum average coverage of contigs to be retained:

Minimum length of contig to be retained as backbone:

The MITObim procedure (mitochondrial baiting and iterative mapping) represents a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads. Labor intensive long-range PCR steps prior to sequencing are no longer required. MITObim is capable of reconstructing mitochondrial genomes without the need of a reference genome of the targeted species by relying solely on (a) mitochondrial genome information of more distantly related taxa or (b) short mitochondrial barcoding sequences (seeds), such as the commonly used cytochrome-oxidase subunit 1 (COI), as a starting reference.

The script is performing three steps and iteratively repeating them: (i) Deriving reference sequence from previous mapping assembly, (ii) in silico baiting using the newly derived reference (iii) previously fished reads are mapped to the newly derived reference leading to an extension of the reference sequence.

For more details please refer to Hahn et al. 2013. Detailed examples are demonstrated in the TUTORIALS section here https://github.com/chrishah/MITObim