Obtaining the Source Code

Procedure

1. Download the following software packages and case files.
   • Download the Bowtie installation package bowtie-1.2.3.zip.

     https://github.com/BenLangmead/bowtie/archive/v1.2.3.zip

   • Download the simde-master installation package simde-master.zip.

     https://codeload.github.com/nemequ/simde/zip/master

   • Download the sse2neon-master installation package sse2neon-master.zip.

     https://codeload.github.com/jratcliff63367/sse2neon/zip/master

   • Download the human genome package chromFa.tar.gz.

     https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

   • Download the SRR742200_1.fastq test case file SRR742200_1.fastq.gz from:

     ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR742/SRR742200/SRR742200_1.fastq.gz

   • Download the SRR742200_2.fastq test case file SRR742200_2.fastq.gz from:

     ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR742/SRR742200/SRR742200_2.fastq.gz

2. Upload the software packages and case files to the server using an SFTP tool.
   • Upload the Bowtie installation package to the /path/to/BOWTIE directory on the server.
   • Upload the simde-master installation package to the /path/to/SIMDE directory on the server.
   • Upload the sse2neon-master installation package to the /path/to/SSE2NENO directory on the server.
   • Upload the chromFa.tar.gz installation package to the /path/to/CHROMFA directory on the server.
   • Upload the SRR742200_1.fastq.gz file to the /path/to/CHROMFA/man_hg19/ directory on the server.
   • Upload the SRR742200_2.fastq.gz file to the /path/to/CHROMFA/man_hg19/ directory on the server.