comparison README.md @ 0:8bbf903bf0cb draft

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Introduction
============

[Kraken] is a taxonomic sequence classifier that assigns taxonomic
labels to short DNA reads. It does this by examining the $k$-mers
within a read and querying a database with those $k$-mers. This database
contains a mapping of every $k$-mer in [Kraken]'s genomic library to the
lowest common ancestor (LCA) in a taxonomic tree of all genomes that
contain that $k$-mer. The set of LCA taxa that correspond to the $k$-mers
in a read are then analyzed to create a single taxonomic label for the
read; this label can be any of the nodes in the taxonomic tree.
[Kraken] is designed to be rapid, sensitive, and highly precise. Our
tests on various real and simulated data have shown [Kraken] to have
sensitivity slightly lower than Megablast with precision being slightly
higher. On a set of simulated 100 bp reads, [Kraken] processed over 1.3
million reads per minute on a single core in normal operation, and over
4.1 million reads per minute in quick operation.

The latest released version of Kraken will be available at the
[Kraken website], and the latest updates to the Kraken source code
are available at the [Kraken GitHub repository].

If you use [Kraken] in your research, please cite the [Kraken paper].
Thank you!

[Kraken]:                     http://ccb.jhu.edu/software/kraken/
[Kraken website]:             http://ccb.jhu.edu/software/kraken/
[Kraken paper]:               http://genomebiology.com/2014/15/3/R46
[Kraken GitHub repository]:   https://github.com/DerrickWood/kraken


System Requirements
===================

Note: Users concerned about the disk or memory requirements should
read the paragraph about MiniKraken, below.

* **Disk space**: Construction of Kraken's standard database will require at
    least 160 GB of disk space. Customized databases may require
    more or less space.  Disk space used is linearly proportional
    to the number of distinct $k$-mers; as of Feb. 2015, Kraken's
    default database contains just under 6 billion (6e9) distinct $k$-mers.

    In addition, the disk used to store the database should be
    locally-attached storage. Storing the database on a network
    filesystem (NFS) partition can cause Kraken's operation to be
    very slow, or to be stopped completely. As NFS accesses are
    much slower than local disk accesses, both preloading and database
    building will be slowed by use of NFS.

* **Memory**: To run efficiently, Kraken requires enough free memory to
    hold the database in RAM. While this can be accomplished using a
    ramdisk, Kraken supplies a utility for loading the database into
    RAM via the OS cache. The default database size is 75 GB (as of
    Feb. 2015), and so you will need at least that much RAM if you want
    to build or run with the default database.

* **Dependencies**: Kraken currently makes extensive use of Linux utilities
    such as sed, find, and wget. Many scripts are written using the
    Bash shell, and the main scripts are written using Perl. Core
    programs needed to build the database and run the classifier are
    written in C++, and need to be compiled using g++.  Multithreading
    is handled using OpenMP.  Downloads of NCBI data are performed by
    wget and in some cases, by rsync.  Most Linux systems that have any
    sort of development package installed will have all of the above
    listed programs and libraries available.

    Finally, if you want to build your own database, you will need to
    install the [Jellyfish] $k$-mer counter.  Note that Kraken only
    supports use of Jellyfish version 1.  Jellyfish version 2 is not
    yet compatible with Kraken.

* **Network connectivity**: Kraken's standard database build and download
    commands expect unfettered FTP and rsync access to the NCBI FTP
    server. If you're working behind a proxy, you may need to set
    certain environment variables (such as `ftp_proxy` or `RSYNC_PROXY`)
    in order to get these commands to work properly.

* **MiniKraken**: To allow users with low-memory computing environments to
    use Kraken, we supply a reduced standard database that can be
    downloaded from the Kraken web site. When Kraken is run with a
    reduced database, we call it MiniKraken.

    The database we make available is only 4 GB in size, and should
    run well on computers with as little as 8 GB of RAM. Disk space
    required for this database is also only 4 GB.

[Jellyfish]:  http://www.cbcb.umd.edu/software/jellyfish/