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/GRCh38_major_release_seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna.gz. All non-primary 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/GRCh38_major_release_seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna.gz -o genomic.fna.gz gunzip genomic.fna.gz awk '{ if ((NR&gt;1)&amp;&amp;($0~/^&gt;/)) { printf("\n%s", $0); } else if (NR==1) { printf("%s", $0); } else { printf("\t%s", $0); } }' genomic.fna | grep -v "^&gt;chr\S*_" - | tr "\t" "\n" &gt; genomic.short.fna bgzip -c genomic.short.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