https://github.com/databio/ref_decoy
Decoy alignment sequences
https://github.com/databio/ref_decoy
Last synced: 4 months ago
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Decoy alignment sequences
- Host: GitHub
- URL: https://github.com/databio/ref_decoy
- Owner: databio
- Created: 2017-01-09T21:38:01.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2022-01-06T21:31:34.000Z (over 4 years ago)
- Last Synced: 2025-09-11T10:15:49.444Z (10 months ago)
- Size: 214 KB
- Stars: 5
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Genome assembly decoy sequences
This repository contains fasta files for pre-alignments. These are useful for studies of repeats, mtDNA, or using as decoy sequences.
## Contents:
### Repeats
* human_alu.fa - Manually curated sequences from GenBank for alu elements.
* human_alphasat.fa - Manually curated sequences from GenBank annotated for centromeric or alpha-satellite DNA repeats.
* human_rDNA.fa - Complete human ribosomal repeat unit
* mouse_rDNA.fa - Complete mouse ribosomal repeat unit (from GenBank).
* human_repeats.fa: a combination of the 3 of above (alu, alphasat, and rDNA) , produced with `cat human_alu.fa human_alphasat.fa human_rDNA.fa > human_repeats.fa`.
### mtDNA
* rCRSd.fa is the Revised Cambridge Reference Sequence (rCRS) of the Human Mitochondrial DNA obtained from [NC_012920](http://www.ncbi.nlm.nih.gov/nuccore/251831106). It is duplicated (pasted 2 times, one right after another) to simulate circular DNA for aligners that do not have a circular setting (hence the appended `d` to the name). This is the assembly used in hg38.
* RSRS.fa is from [this paper](http://dx.doi.org/10.1016/j.ajhg.2012.03.002).
* eve1.fa is from [this paper](http://dx.doi.org/10.1093/nar/gkm207).
* human_chrM2x - Doubled chrM derived from [AF347015](http://www.ncbi.nlm.nih.gov/nuccore/13273284), the African Yoruban sequence used in the hg19 assembly.
* mouse_chrM2x - Doubled chrM derived from mm10 reference.
## Pre-built indexes
You can download pre-built [refgenie](http://www.github.com/databio/refgenie) reference genomes indexes for use in pipelines here:
* [list of pre-built indexes](http://big.databio.org/refgenomes/)
To use these with [pypiper](http://www.databio.org/pypiper) pipelines, just unzip the folder and place in your genomes folder (e.g. `$GENOMES`).
## Built it yourself
Build genome references for these decoy sequences using [refgenie](http://github.com/databio/refgenie) like this:
```
refgenie.py -i hg19_alphasat.fa
```
A complete setup:
```
GENOMES=decoy_genomes
pip install --user --upgrade https://github.com/epigen/pypiper/zipball/master
git clone https://github.com/databio/ref_decoy.git
git clone https://github.com/databio/refgenie.git
for fa_file in `ls ref_decoy/*.fa`; do python refgenie/src/refgenie.py -i $fa_file; done
```
Or, using the refgenie docker image (adds `-d`):
```
for fa_file in `ls ref_decoy/*.fa`; do python refgenie/src/refgenie.py -d -i $fa_file; done
```