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https://github.com/adamtaranto/te-insertion-scanner
Scan whole genome alignments for signatures of transposon insertion.
https://github.com/adamtaranto/te-insertion-scanner
Last synced: 2 months ago
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Scan whole genome alignments for signatures of transposon insertion.
- Host: GitHub
- URL: https://github.com/adamtaranto/te-insertion-scanner
- Owner: Adamtaranto
- License: mit
- Created: 2017-04-11T13:35:41.000Z (almost 8 years ago)
- Default Branch: main
- Last Pushed: 2024-11-04T23:33:13.000Z (3 months ago)
- Last Synced: 2024-11-05T00:26:26.509Z (3 months ago)
- Language: Python
- Size: 22.5 KB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Tinscan: TE-Insertion-Scanner
Scan whole genome alignments for transposon insertion signatures.
# Table of contents
* [Algorithm overview](#algorithm-overview)
* [Options and usage](#options-and-usage)
* [Installing Tinscan](#installing-tinscan)
* [Example usage](#example-usage)
# Algorithm overview
1. Perform gapped and chained whole genome alignment of query genome B onto target genome A.
2. Where two aligned segments are contiguous in B (or separated by no more than --qGap), and
3. Separated by an insertion in the range --minInsert:--maxInsert in A, and
4. At least one flanking alignment in A satisfies the threshold --minIdent, and differs from its mate by no more than --maxIdentDiff %
5. Log flanks and candidate insertion.
6. Attempt to infer TSDs from the internal overlap of flanking alignments in B genome.
# Options and usage
### Installing Tinscan
Requirements:
* [LASTZ](http://www.bx.psu.edu/~rsharris/lastz/) genome alignment tool from the Miller Lab, Penn State.
* Biopython
You can set up a conda environment with the required dependencies using the YAML files in this repo:
For ARM64 (Apple Silicon Macs) create a virtual intel env.
```bash
# For ARM64 Macs only
conda env create -f env_osx64.yml
conda activate tinscan-osx64
```
For all other operating systems use `environment.yml`
```bash
conda env create -f environment.yml
conda activate tinscan
```
With the conda env active you can now install tinscan.
1) Install from PyPi.
```bash
pip install tinscan
```
2) For the latest development version, clone and install from this repository.
```bash
git clone https://github.com/Adamtaranto/TE-insertion-scanner.git && cd TE-insertion-scanner && pip install -e ".[tests]"
```
### Example usage
Find insertion events in genome A (target) relative to genome B (query).
**Prepare Input Genomes**
Split A and B genomes into two directories containing one scaffold per file.
Check that sequence names are unique within genomes.
```bash
tinscan-prep --adir data/A_target_split --bdir data/B_query_split\
-A data/A_target_genome.fasta -B data/B_query_genome.fasta
```
Output:
data/A_target_split/*.fa
data/B_query_split/*.fa
**Align Genomes**
Align each scaffold from genome B onto each genome A scaffold.
Report alignments with >= 60% identity and length >= 100bp.
```bash
tinscan-align --adir data/A_target_split --bdir data/B_query_split \
--outdir A_Inserts --outfile A_Inserts_vs_B.tab \
--minIdt 60 --minLen 100 --hspthresh 3000
```
Output:
A_Inserts/A_Inserts_vs_B.tab
*Note:* Alignment tasks can be limited to a specified set of pairwise comparisons
where appropriate (i.e. when homologous chromosome pairs are known between
assemblies) using the option `--pairs`.
Comparisons are specified with a
tab-delimited text file, where column 1 contains sequence names from genome A, and
column 2 contains sequences from genome B.
In the example *Chromosome_pairs.txt*, Chr A2 has been assembled
as two scaffolds (B2, B3) in genome B.
```
#Chromosome_pairs.txt
A1 B1
A2 B2
A2 B3
A3 B4
```
**Find Insertions**
Scan alignments for insertion events and report as GFF annotation of Genome A
```bash
tinscan-find --infile A_Inserts/A_Inserts_vs_B.tab \
--outdir A_Inserts --gffOut A_Inserts_vs_B_l100_id80.gff3 \
--maxInsert 50000 --minIdent 80 --maxIdentDiff 20
```
Output:
A_Inserts/A_Inserts_vs_B_l100_id80.gff3
# License
Software provided under MIT license.