GRCh38.p13 Reference FASTA (bgzip'd with faidx)

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. 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/^&gt;(NC.*Homo sapiens chromosome ([0-9XY]+),.*)/&gt;chr\2 \1/g' | sed -r 's/^&gt;(NC.*Homo sapiens mitochondrion,.*)/&gt;chrM \1/g' &gt; chrfix.fna bgzip -c chrfix.fna &gt; 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