Pre-built aligner indexes for CHM13 using UCSC-style "chr1" chromosome names as sequence names

Software versions used:

Hisat2:
        hisat2-align-s version 2.1.0
        64-bit
        Built on login-node03
        Wed Jun  7 15:53:42 EDT 2017
        Compiler: gcc version 4.8.2 (GCC) 
        Options: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY

Bowtie2:
        bowtie2-align-s version 2.3.4.3
        64-bit
        Built on default-985f7a91-f7b9-4ecf-bdfc-9e83887f2387
        Thu Sep 20 02:27:06 UTC 2018
        Compiler: gcc version 4.8.2 20140120 (Red Hat 4.8.2-15) (GCC) 
        Options: -O3 -m64 -msse2 -funroll-loops -g3  -DBOOST_MATH_DISABLE_FLOAT128 -m64 -fPIC -std=c++98 -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1

BWA-MEM2:
        2.0pre2, AVX2 build

minimap2:
        2.17-r941

Indexes were built with the following commands:

zcat ../../GCA_009914755.4.chrNames.fa.gz > GCA_009914755.4.chrNames.fa

mkdir GCA_009914755.4.chrNames-minimap2
mkdir GCA_009914755.4.chrNames-bowtie2
mkdir GCA_009914755.4.chrNames-hisat2
mkdir GCA_009914755.4.chrNames-bwa-mem2

for i in *; do cd $i; ln -s ../*.fa; cd ..; done

cd GCA_009914755.4.chrNames-bowtie2; nohup bowtie2-build GCA_009914755.4.chrNames.fa GCA_009914755.chrNames.4 --threads 8 &> bowtie2-out.txt & ; cd ..
cd GCA_009914755.4.chrNames-hisat2; nohup hisat2-build -p 8 GCA_009914755.chrNames.4.fa GCA_009914755.chrNames.4 &> hisat2-out.txt & ; cd ..
cd GCA_009914755.4.chrNames-bwa-mem2; nohup bwa-mem2.avx2 index GCA_009914755.4.chrNames.fa  &> bwa-mem-out.txt & ; cd ..
cd GCA_009914755.4.chrNames-minimap2; nohup minimap2 GCA_009914755.4.chrNames.fa -d GCA_009914755.4.chrNames.idx &> minimap2-out.txt & ; cd ..

tar cvfz chm13-chrNames-minimap2.tgz GCA_009914755.4*-minimap2/*
tar cvfz chm13-chrNames-bwa-mem2.tgz GCA_009914755.4*-bwa-mem2/* &
tar cvfz chm13-chrNames-bowtie2.tgz GCA_009914755.4*-bowtie2/* &
tar cvfz chm13-chrNames-hisat2.tgz GCA_009914755.4*-hisat2/* &

rm -rf GCA_*-*