GRCh38.p13 Reference FASTA (bgzip'd with faidx)
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This is derived from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz. A short name (chr1, chr2, ... chr22, chrX, chrY, chrM) has been added to each primary chromosomal sequence. All other sequences have been removed. It has then been recompressed with bgzip and indexed with samtools: <pre><code class="language-bash">curl -#fSL https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.fna.gz -o genomic.fna.gz gunzip genomic.fna.gz cat genomic.fna | sed -r 's/^>(NC.*Homo sapiens chromosome ([0-9XY]+),.*)/>chr\2 \1/g' | sed -r 's/^>(NC.*Homo sapiens mitochondrion,.*)/>chrM \1/g' > chrfix.fna awk '{ if ((NR>1)&&($0~/^>/)) { printf("\n%s", $0); } else if (NR==1) { printf("%s", $0); } else { printf("\t%s", $0); } }' chrfix.fna | grep ">chr" - | tr "\t" "\n" > chrfix.short.fna bgzip -c chrfix.short.fna > reference.fna.bgz samtools faidx reference.fna.bgz tar -czvf GRCh38_reference_fasta.tar reference.fna.bgz reference.fna.bgz.fai reference.fna.bgz.gzi </code></pre> This tar file contains: reference.fna.bgz reference.fna.bgz.fai reference.fna.bgz.gzi
