Recommended query genomes and FTP URLs - Githubissues

syueqiao / logan_unsticker

Short script to remove sticky sequences from a protein DB against input genomes/fasta files of choice.

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Recommended query genomes and FTP URLs #1

Open syueqiao opened 1 month ago

syueqiao commented 1 month ago

Extrapolated from common sequencing targets from the SRA, and sequences that returned false positives during initial database screenings:

Human genome - integration sites: https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.2bit
Mouse genome - integration sites: https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.2bit
E. coli genome - common bacterial genes: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz -Streptococcus pyogenes genome - fibronectin-binding genes: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/475/035/GCF_900475035.1_41965_F01/GCF_900475035.1_41965_F01_genomic.fna.gz
Yeast genome - common eukaryote genes: https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/sacCer3.2bit

syueqiao commented 1 month ago

Additional recommended screening genomes will be updated as FP arise.