Module: NUMTFinder Description: Nuclear mitochondrial fragment (NUMT) search tool Version: 0.5.2 Last Edit: 21/03/22 Citation: Edwards RJ et al. (2021), BMC Genomics GitHub: https://github.com/slimsuite/numtfinder

Copyright © 2021 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_obj rje_rmd rje_seqlist rje_samtools gablam

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

NUMTFinder uses a mitochondrial genome to search against genome assembly and identify putative NUMTs. NUMT fragments are then combined into NUMT blocks based on proximity.

The general NUMTFinder workflow is:

1. Generate a double-copy linearised mtDNA sequence from the circular genome. 2. Perform a BLAST+ blastn search of the double-mtDNA versus the genome assembly using GABLAM. 3. Optionally filter short NUMT hits based on length. 4. Optionally filter NUMT hits based on hit sequence name and/or high identity (e.g. identify/remove real mtDNA). 5. Collapse nearby fragments into NUMT blocks. By default, fragments can incorporate duplications and rearrangements, including inversions. Setting stranded=T will restrict blocks to fragments on the same strand. 6. Map fragments back on to the mtDNA genome and output a coverage plot.

Plans for future releases include:

• incorporation of additional search methods (LASTZ or kmers)
• assembly masking options
• options to restrict NUMT blocks to fully collinear hits.
• automated running of Diploidocus long-read regcheck on fragments and blocks

Commandline

Main NUMTFinder run options

seqin=FILE : Genome assembly in which to search for NUMTs []
mtdna=FILE : mtDNA reference genome to use for search []
basefile=X : Prefix for output files [numtfinder]
summarise=T/F : Whether to summarise input sequence files upon loading [True]
dochtml=T/F : Generate HTML NUMTFinder documentation (*.docs.html) instead of main run [False]

NUMTFinder search options

circle=T/F : Whether the mtDNA is circular [True]
blaste=X : BLAST+ blastn evalue cutoff for NUMT search [1e-4]
minfraglen=INT : Minimum local (NUMT fragment) alignment length (sets GABLAM localmin=X) [0]
exclude=LIST : Exclude listed sequence names from search [mtDNA sequence name]
mtmaxcov=PERC : Maximum percentage coverage of mtDNA (at mtmaxid identity) to allow [99]
mtmaxid=PERC : Maximum percentage identity of mtDNA hits > mtmaxcov coverage to allow [99]
mtmaxexclude=T/F: Whether add sequences breaching mtmax filters to the exclude=LIST exclusion list [True]
keepblast=T/F : Whether to keep the blast results files rather than delete them [True]
forks=INT : Use multiple threads for the NUMT search [0]

NUMTFinder block options

fragmerge=X : Max Length of gaps between fragmented local hits to merge [8000]
stranded=T/F : Whether to only merge fragments on the same strand [False]

NUMTFinder output options

localgff=T/F : Whether to output GFF format files of the NUMT hits against the genome [True]
localsam=T/F : Whether to output SAM format files of the NUMT hits against the genome [True]
fasdir=PATH : Directory in which to save fasta files [numtfasta/]
fragfas=T/F : Whether to output NUMT fragment to fasta file [True]
fragrevcomp=T/F : Whether to reverse-complement DNA fragments that are on reverse strand to query [True]
blockfas=T/F : Whether to generate a combined fasta file of NUMT block regions (positive strand) [True]
nocovfas=T/F : Whether to output the regions of mtDNA with no coverage & peak coverage [False]
depthplot=T/F : Whether to output mtDNA depth plots of sequence coverage (requires R) [True]
depthsmooth=X : Smooth out any read plateaus < X nucleotides in length [0]
peaksmooth=X : Smooth out Xcoverage peaks < X depth difference to flanks (<1 = %Median) [0]

History Module Version History

    # 0.0.0 - Initial Compilation.
    # 0.1.0 - Added dochtml=T and modified docstring for standalone git repo.
    # 0.1.1 - Fixed bug with default fragmerge=INT. Now set to 8kb.
    # 0.2.0 - Added SAM output and depth profile of coverage across mitochondrion.
    # 0.3.0 - Added additional exclusion, flagging and filtering of possible mtDNA.
    # 0.4.0 - Added output of zero-coverage mtDNA regions, block fasta, and coverage summary.
    # 0.4.1 - Fixed bug when no NUMTs. Added a bit more documentation of output.
    # 0.4.2 - Fixed coverage output bugs for -ve strand hits over circularisation spot. Improved pickup of partial run.
    # 0.5.0 - Modified depth plot defaults to remove the smoothing.
    # 0.5.1 - Fixed bug with peak fasta output.
    # 0.5.2 - Fixed bug with circle=F mtDNA.