Bowtie: an Ultrafast, Lightweight Short Read Aligner

Bowtie Getting Started Guide
============================

 Download and extract the appropriate Bowtie binary release from
 http://bowtie-bio.sf.net into a fresh directory. Change to that
 directory.

 Performing alignments
 ---------------------

 The Bowtie source and binary packages come with a pre-built index of
 the E. coli genome, and a set of 1,000 35-bp reads simulated from that
 genome. To use Bowtie to align those reads, issue the following
 command.  If you get an error message "command not found", try adding
 a "./" before the "bowtie".
 
    bowtie e_coli reads/e_coli_1000.fq

 The first argument to bowtie is the basename of the index for the
 genome to be searched. The second argument is the name of a FASTQ file
 containing the reads.

 Depending on your computer, the run might take a few seconds up to
 about a minute. You will see bowtie print many lines of output. Each
 line is an alignment for a read. The name of the aligned read appears
 in the leftmost column. The final line should say "Reported 698
 alignments to 1 output stream(s)" or something similar. 

 Next, issue this command:

    bowtie -t e_coli reads/e_coli_1000.fq e_coli.map

 This run calculates the same alignments as the previous run, but the
 alignments are written to e_coli.map (the final argument) rather than
 to the screen. Also, the -t option instructs Bowtie to print timing
 statistics.  The output should look something like this:

    Time loading forward index: 00:00:00
    Time loading mirror index: 00:00:00
    Seeded quality full-index search: 00:00:00
    # reads processed: 1000
    # reads with at least one reported alignment: 699 (69.90%)
    # reads that failed to align: 301 (30.10%)
    Reported 699 alignments to 1 output stream(s)
    Time searching: 00:00:00
    Overall time: 00:00:00

 Installing a pre-built index
 ----------------------------

 Download the pre-built S. cerevisiae genome package from the Bowtie
 FTP site:

    ftp://ftp.cbcb.umd.edu/pub/data/bowtie_indexes/s_cerevisiae.ebwt.zip

 All pre-built indexes are packaged as .zip archives, and the S.
 cerevisiae archive is named s_cerevisiae.ebwt.zip. When it has
 finished downloading, extract the archive into the Bowtie 'indexes'
 subdirectory using your preferred unzip tool. The index is now
 installed.

 To test that the index is properly installed, issue this command from
 the Bowtie install directory:

    bowtie -c s_cerevisiae ATTGTAGTTCGAGTAAGTAATGTGGGTTTG

 This command searches the S. cerevisiae index with a single read. The
 -c argument instructs Bowtie to obtain read sequences directly from
 the command line rather than from a file. If the index is installed
 properly, this command should print a single alignment and then exit.

 If you would rather install pre-built indexes somewhere other than the
 'indexes' subdirectory of the Bowtie install directory, simply set the
 BOWTIE_INDEXES environment variable to point to your preferred
 directory and extract indexes there instead.

 Building a new index
 --------------------

 The pre-built E. coli index included with Bowtie is built from the
 sequence for strain 536, known to cause urinary tract infections. We
 will create a new index from the sequence of E. coli strain O157:H7, a
 strain known to cause food poisoning. Download the sequence file from:

    ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7/NC_002127.fna

 When the sequence file is finished downloading, move it to the Bowtie
 install directory and issue this command:

    bowtie-build NC_002127.fna e_coli_O157_H7

 The command should finish quickly, and print several lines of status
 messages. When the command has completed, note that the current
 directory contains four new files named e_coli_O157_H7.1.ebwt,
 e_coli_O157_H7.2.ebwt, e_coli_O157_H7.rev.1.ebwt, and
 e_coli_O157_H7.rev.2.ebwt. These files constitute the index. Move
 these files to the indexes subdirectory to install it.

 To test that the index is properly installed, issue this command:

    bowtie -c e_coli_O157_H7 GCGTGAGCTATGAGAAAGCGCCACGCTTCC

 If the index is installed properly, this command should print a single
 alignment and then exit.

 Finding variations with SAMtools
 --------------------------------

 SAMtools (http://samtools.sf.net) is a suite of tools for storing,
 manipulating, and analyzing alignments such as those output by Bowtie.
 SAMtools understands alignments in either of two complementary
 formats: the human-readable SAM format, or the binary BAM format.
 Because Bowtie can output SAM (using the -S/--sam option), and SAM can
 can be converted to BAM using SAMtools, Bowtie users can make full use
 of the analyses implemented in SAMtools, or in any other tools
 supporting SAM or BAM.

 We will use SAMtools to find SNPs in a set of simulated reads included
 with Bowtie.  The reads cover the first 10,000 bases of the pre-built
 E. coli genome and contain 10 SNPs throughout.  First, we run 'bowtie'
 to align the reads, being sure to specify the -S option.  We also
 specify an output file that we will use as input for the next step
 (though pipes can be used to accomplish the same thing without the
 intermediate file):

    bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam

 Next, we convert the SAM file to BAM in preparation for sorting.  We
 assume that SAMtools is installed and that the samtools binary is
 accessible in the PATH.

    samtools view -bS -o ec_snp.bam ec_snp.sam
 
 Next, we sort the BAM file, in preparation for SNP calling:

    samtools sort ec_snp.bam ec_snp.sorted
 
 We now have a sorted BAM file called ec_snp.sorted.bam.  Sorted BAM is
 a useful format because the alignments are both compressed, which is
 convenient for long-term storage, and sorted, which is conveneint for
 variant discovery.  Finally, we call variants from the Sorted BAM:
 
    samtools pileup -cv -f genomes/NC_008253.fna ec_snp.sorted.bam

 For this sample data, the 'samtools pileup' command should print
 records for 10 distinct SNPs, the first being at position 541 in the
 reference.

 See the SAMtools web site for details on how to use these and other
 tools in the SAMtools suite: http://samtools.sf.net/.