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https://github.com/adamtaranto/mimeo

Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.
https://github.com/adamtaranto/mimeo

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Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.

Host: GitHub
URL: https://github.com/adamtaranto/mimeo
Owner: Adamtaranto
License: mit
Created: 2017-09-06T02:57:48.000Z (over 7 years ago)
Default Branch: master
Last Pushed: 2024-11-03T11:49:18.000Z (3 months ago)
Last Synced: 2024-11-03T12:26:57.621Z (3 months ago)
Language: Python
Size: 46.9 KB
Stars: 1
Watchers: 3
Forks: 2
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

# Mimeo

# Table of contents

* [Modules](#modules)
* [Installing Mimeo](#installing-mimeo)
* [Example usage](#example-usage)
* [Standard options](#standard-options)
* [mimeo-self](#mimeo-self)
* [mimeo-x](#mimeo-x)
* [mimeo-map](#mimeo-map)
* [mimeo-filter](#mimeo-filter)
* [Alternative alignment engines](#importing-alignments)
* [License](#license)

# Modules

Mimeo comprises three tools for parsing repeats from whole-genome alignments:

## mimeo-self

**Internal repeat finder.** Mimeo-self aligns a genome to itself and extracts high-identity segments above
a coverage threshold. This method is less sensitive to disruption by indels and repeat-directed point mutations than
kmer-based methods such as RepeatScout. Reported annotations indicate overlapping segments above the coverage threshold,
mimeo-self does not attempt to separate nested repeats. Use this tool to identify candidate repeat regions for curated annotation.

## mimeo-x

**Cross-species repeat finder.** A newly acquired or low-copy transposon may slip past copy-number based annotation tools. Mimeo-x searches for features which are abundant in an external reference genome, allowing for
annotation of complete elements as they occur in a horizontal-transfer donor species, or of conserved coding segments
of related transposon families.

## mimeo-map

**Find all high-identity segments shared between genomes.** Mimeo-map identifies candidate horizontally
transferred segments between sufficiently diverged species. When comparing isolates of a single species, aligned segments correspond to directly homologous sequences and internally repetitive features.

Intra/Inter-genomic alignments from Mimeo-self or Mimeo-x can be reprocessed with Mimeo-map to generate annotations of
unfiltered/uncollapsed alignments. These raw alignment annotations can be used to interrogate repetitive-segments for coverage breakpoints corresponding to nested transposons with differing abundances across the genome.

## mimeo-filter

An additional tool **mimeo-filter** is now included to allow post-filtering of SSR-rich sequences from FASTA formatted
candidate-repeat libraries.

# Installing Mimeo

Requirements:
* [LASTZ](http://www.bx.psu.edu/~rsharris/lastz/) genome alignment tool from the Miller Lab, Penn State.
* [bedtools](http://bedtools.readthedocs.io/en/latest/content/installation.html)
* [trf](https://tandem.bu.edu/trf/trf.html)

Install from Bioconda:
```bash
conda install mimeo
```

Install from PyPi:
```bash
pip install mimeo
```

Clone and install from this repository:
```bash
git clone https://github.com/Adamtaranto/mimeo.git && cd mimeo && pip install -e .
```

# Example usage

### mimeo-self

Annotate features in genome A which are > 100bp and occur with >=
80% identity at least 3 times on other scaffolds OR at least 4 times
on the same scaffold.

```bash
mimeo-self --adir data/A_genome_Split --afasta data/A_genome.fasta \
-d MS_outdir --gffout A_genome_Inter3_Intra4_id80_len_100.gff3 \
--outfile A_genome_Self_Align.tab --label A_Rep3 --prefix A_Self --minIdt 80 \
--minLen 100 --minCov 3 --intraCov 4 --strictSelf
```

Output:
- MS_outdir/A_genome_Inter3_Intra4_id80_len_100.gff3
- MS_outdir/A_genome_Self_Align.tab
- data/A_genome_Split/*.fa

### mimeo-x

Annotate features in genome A which are > 100bp and occur with >=
80% identity at least 5 times in genome B.

```bash
mimeo-x --afasta data/A_genome.fasta --bfasta data/B_genome.fasta \
-d MX_outdir --gffout B_Rep5_in_A.gff3 --outfile B_Reps_in_A_id80_len100.tab \
--label B_Rep5 --prefix B_Rep5 --minIdt 80 --minLen 100 --minCov 5
```

Output:
- MX_outdir/B_Rep5_in_A.gff3
- MX_outdir/B_Reps_in_A_id80_len100.tab

### mimeo-map

Annotate features in genome A which are > 100bp and occur with >=
90% identity in genome B. No coverage filter, all alignments are reported.

```bash
mimeo-map --afasta data/A_genome.fasta --bfasta data/B_genome.fasta \
-d MM_outdir --gffout B_in_A_id90.gff3 --outfile B_in_A_id90.tab \
--label B_90 --prefix B_90 --minIdt 90 --minLen 100
```

Output:
- MM_outdir/B_in_A_id90.gff3
- MM_outdir/B_in_A_id90.tab

### mimeo-map + SSR filter

Annotate features in genome A which are > 100bp and occur with >=
98% identity in genome B. Reuse B to A-genome alignment from the previous run.

Filter out hits which are >= 40% tandem repeats. Write filtered hits
as tab file and GFF3 annotation.

```bash
mimeo-map --afasta data/A_genome.fasta --bfasta data/B_genome.fasta \
-d MM_outdir --gffout B_in_A_id98_maxSSR40.gff3 --outfile B_in_A_id98.tab \
--label B_98 --prefix B_98 --minIdt 98 --minLen 100 \
--recycle --maxtandem 40 --writeTRF
```

Output:
- MM_outdir/B_in_A_id98_maxSSR40.gff3
- MM_outdir/B_in_A_id98.tab.trf

### mimeo-filter

Filter sequences comprised of >= 40% short tandem repeats from a multifasta
library of candidate transposons.

```bash
mimeo-filter --infile data/candidate_TEs.fa
```

Output:
- candidate_TEs_filtered.fa

# Standard options

### mimeo-self

```
Usage: mimeo-self [-h] [--adir ADIR] [--afasta AFASTA] [-r] [-d OUTDIR]
[--gffout GFFOUT] [--outfile OUTFILE] [--verbose]
[--label LABEL] [--prefix PREFIX] [--lzpath LZPATH]
[--bedtools BEDTOOLS] [--minIdt MINIDT] [--minLen MINLEN]
[--minCov MINCOV] [--hspthresh HSPTHRESH]
[--intraCov INTRACOV] [--strictSelf]

Internal repeat finder. Mimeo-self aligns a genome to itself and extracts
high-identity segments above a coverage threshold.

Optional arguments:
-h, --help Show this help message and exit.
--adir Name of the directory containing sequences from the genome.
Write split files here if providing genome as
multifasta.
--afasta Genome as multifasta.
-r, --recycle Use existing alignment "--outfile" if found.
-d , --outdir Write output files to this directory. (Default: cwd)
--gffout Name of GFF3 annotation file.
--outfile Name of alignment result file.
--verbose If set report LASTZ progress.
--label Set annotation TYPE field in gff.
--prefix ID prefix for internal repeats.
--lzpath Custom path to LASTZ executable if not in $PATH.
--bedtools Custom path to bedtools executable if not in $PATH.
--minIdt Minimum alignment identity to report.
--minLen Minimum alignment length to report.
--minCov Minimum depth of aligned segments to report repeat
feature.
--hspthresh Set HSP min score threshold for LASTZ.
--intraCov Minimum depth of aligned segments from the same scaffold
to report feature. Used if "--strictSelf" mode is
selected.
--strictSelf If set process same-scaffold alignments separately
with the option to use higher "--intraCov" threshold.
Sometimes useful to avoid false repeat calls from
staggered alignments over SSRs or short tandem
duplication.
```

### mimeo-x

```
Usage: mimeo-x [-h] [--adir ADIR] [--bdir BDIR] [--afasta AFASTA]
[--bfasta BFASTA] [-r] [-d OUTDIR] [--gffout GFFOUT]
[--outfile OUTFILE] [--verbose] [--label LABEL]
[--prefix PREFIX] [--lzpath LZPATH] [--bedtools BEDTOOLS]
[--minIdt MINIDT] [--minLen MINLEN] [--minCov MINCOV]
[--hspthresh HSPTHRESH]

Cross-species repeat finder. Mimeo-x searches for features which are abundant
in an external reference genome.

### mimeo-map

```
Usage: mimeo-map [-h] [--adir ADIR] [--bdir BDIR] [--afasta AFASTA]
[--bfasta BFASTA] [-r] [-d OUTDIR] [--gffout GFFOUT]
[--outfile OUTFILE] [--verbose] [--label LABEL]
[--prefix PREFIX] [--keeptemp] [--lzpath LZPATH]
[--minIdt MINIDT] [--minLen MINLEN] [--hspthresh HSPTHRESH]
[--TRFpath TRFPATH] [--tmatch TMATCH] [--tmismatch TMISMATCH]
[--tdelta TDELTA] [--tPM TPM] [--tPI TPI]
[--tminscore TMINSCORE] [--tmaxperiod TMAXPERIOD]
[--maxtandem MAXTANDEM] [--writeTRF]

Find all high-identity segments shared between genomes.

Optional arguments:
-h, --help Show this help message and exit.
--adir Name of the directory containing sequences from A genome.
--bdir Name of the directory containing sequences from B genome.
--afasta A genome as multifasta.
--bfasta B genome as multifasta.
-r, --recycle Use existing alignment "--outfile" if found.
-d, --outdir Write output files to this directory. (Default: cwd)
--gffout Name of GFF3 annotation file. If not set, suppress
output.
--outfile Name of alignment result file.
--verbose If set report LASTZ progress.
--label Set annotation TYPE field in GFF.
--prefix ID prefix for B-genome hits annotated in A-genome.
--keeptemp If set does not remove temp files.
--lzpath Custom path to LASTZ executable if not in $PATH.
--minIdt Minimum alignment identity to report.
--minLen Minimum alignment length to report.
--hspthresh Set HSP min score threshold for LASTZ.
--TRFpath Custom path to TRF executable if not in $PATH.
--tmatch TRF matching weight.
--tmismatch TRF mismatching penalty.
--tdelta TRF indel penalty.
--tPM TRF match probability.
--tPI TRF indel probability.
--tminscore TRF minimum alignment score to report.
--tmaxperiod TRF maximum period size to report.
--maxtandem Max percentage of an A-genome alignment which may be masked by TRF.
If exceeded, the alignment will be discarded.
--writeTRF If set write TRF filtered alignment file for use with
other mimeo modules.
```

### mimeo-filter

```
Usage: mimeo-filter [-h] --infile INFILE [-d OUTDIR] [--outfile OUTFILE]
[--keeptemp] [--verbose] [--TRFpath TRFPATH]
[--tmatch TMATCH] [--tmismatch TMISMATCH]
[--tdelta TDELTA] [--tPM TPM] [--tPI TPI]
[--tminscore TMINSCORE] [--tmaxperiod TMAXPERIOD]
[--maxtandem MAXTANDEM]

Filter SSR containing sequences from FASTA library of repeats.

Optional arguments:
-h, --help Show this help message and exit.
--infile Name of the directory containing sequences from A genome.
-d, --outdir Write output files to this directory. (Default: cwd)
--outfile Name of alignment result file.
--keeptemp If set does not remove temp files.
--verbose If set report LASTZ progress.
--TRFpath Custom path to TRF executable if not in $PATH.
--tmatch TRF matching weight
--tmismatch TRF mismatching penalty.
--tdelta TRF indel penalty.
--tPM TRF match probability.
--tPI TRF indel probability.
--tminscore TRF minimum alignment score to report.
--tmaxperiod TRF maximum period size to report. Note: Setting this
score too high may exclude some LTR retrotransposons.
Optimal len to exclude only SSRs is 10-50bp.
--maxtandem Max percentage of a sequence which may be masked by
TRF. If exceeded, the element will be discarded.

```

# Importing alignments

Whole genome alignments generated by alternative tools (i.e. BLAT) can be provided to any of the Mimeo modules
as a tab-delimited file with the columns:

```
[1] name1 = Name of target sequence in genome A
[2] strand1 = Strand of alignment in target sequence
[3] start1 = 5-prime position of alignment in target (lower value irrespective of strand)
[4] end1 = 3-prime position of alignment in target (higher value irrespective of strand)
[5] name2 = Name of source sequence in genome B
[6] strand2 = Strand of alignment in source
[7] start2+ = 5-prime position of alignment in source (lower value irrespective of strand)
[8] end2+ = 3-prime position of alignment in source (higher value irrespective of strand)
[9] score = Alignment score as int
[10] identity = Identity of alignment as float
```

File should be sorted by columns 1,3,4

# License

Software provided under MIT license.