This repository contains fasta files for pre-alignments. These are useful for studies of repeats, mtDNA, or using as decoy sequences.
- 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.
- rCRSd.fa is the Revised Cambridge Reference Sequence (rCRS) of the Human Mitochondrial DNA obtained from NC_012920. 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
dto the name). This is the assembly used in hg38. - RSRS.fa is from this paper.
- eve1.fa is from this paper.
- human_chrM2x - Doubled chrM derived from AF347015, the African Yoruban sequence used in the hg19 assembly.
- mouse_chrM2x - Doubled chrM derived from mm10 reference.
You can download pre-built refgenie reference genomes indexes for use in pipelines here:
To use these with pypiper pipelines, just unzip the folder and place in your genomes folder (e.g. $GENOMES).
Build genome references for these decoy sequences using 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