Pre-built aligner indexes for CHM13

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:

twoBitToFa ../GCA_009914755.4.2bit ./GCA_009914755.4.fa

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

mkdir GCA_009914755.4-minimap2
mv *.idx GCA_009914755.4-minimap2

mkdir GCA_009914755.4-bowtie2
mv *.bt2 *.sa GCA_009914755.4-bowtie2/

mkdir GCA_009914755.4-hisat2
mv *.ht2 GCA_009914755.4-hisat2

mkdir GCA_009914755.4-bwa-mem2
mv *.0123 *.pac *.ann *.amb GCA_009914755.4-bwa-mem2/

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

      Name                                                 Last modified      Size  Description
      Parent Directory                                                          -   
      bowtie2-out.txt                                      2022-04-05 03:37   62K  
      bowtie2.tgz                                          2022-04-05 04:16  3.6G  
      bwa-mem2-out.txt                                     2022-04-05 03:46  518   
      bwa-mem2.tgz                                         2022-04-05 06:16   56G  
      hisat2-out.txt                                       2022-04-05 03:27  6.2K  
      hisat2.tgz                                           2022-04-05 04:16  4.1G  
      minimap2-out.txt                                     2022-04-05 03:19  559   
      minimap2.tgz                                         2022-04-05 03:39  3.8G