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SamahElmahdi / Glaucoma-variant-calling

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#14 searching for indexed refseq #14

Open marwaaswa opened 4 years ago

marwaaswa commented 4 years ago

-searching for indexed reference genome to decrease computational resources needed for indexing

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/ (in readme analysis :

HISAT2 index files

GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.hisat2_index.tar.gz GCA_000001405.15_GRCh38_full_analysis_set.fna.hisat2_index.tar.gz GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna.hisat2_index.tar.gz GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna.hisat2_index.tar.gz

tar archives containing HISAT2 index files for the analysis sets. The HISAT2 index files were generated by running HISAT2 version 2.0.5 using the default parameters for the index command.

Annotation files

marwaaswa commented 4 years ago

https://www.ncbi.nlm.nih.gov/projects/CCDS/CcdsBrowse.cgi?REQUEST=ALLFIELDS&DATA=&ORGANISM=9606&BUILDS=CURRENTBUILDS ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human