Commit 5e14db80 authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

New upstream version 2.2+dfsg

parent 32193931

README.md

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Mash is normally distributed as a dependency-free binary for Linux or OSX (see

https://github.com/marbl/Mash/releases). This source distribution is intended

for other operating systems or for development. Mash requires c++11 to build,

which is available in and GCC >= 4.8 and OSX >= 10.7.

for other operating systems or for development. Mash requires c++14 to build,

which is available in and GCC >= 5 and XCode >= 6.



See http://mash.readthedocs.org for more information.

doc/sphinx/conf.py

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@@ -43,7 +43,7 @@ source_suffix = '.rst' 
master_doc = 'index'



# General information about the project.

project = u'mash'

project = u'Mash'

copyright = u'2015, Brian Ondov, Todd Treangen, Adam Phillippy'



# The version info for the project you're documenting, acts as replacement for

doc/sphinx/data.rst

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@@ -37,24 +37,6 @@ Figure 5: 
 * `fig5.html <https://obj.umiacs.umd.edu/mash/screen/fig5/fig5.html>`_: Interactive version

 * `fig5.tsv <https://obj.umiacs.umd.edu/mash/screen/fig5/fig5.tsv>`_: Source data



Public data sources

~~~~~~~~~~~~~~~~~~~



The BLAST ``nr`` database was downloaded from ``ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*``.



HMP data were downloaded from ``ftp://public-ftp.ihmpdcc.org/``, reads from the ``Ilumina/`` directory

and coding sequences from the ``HMGI/`` directory. Within these folders, sample SRS015937 resides in

``tongue_dorsum/`` and SRS020263 in ``right_retroauricular_crease/``.



SRA runs downloaded with the `SRA Toolkit <https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/>`_.



RefSeq genomes downloaded from the ``genomes/refseq/`` directory of ``ftp.ncbi.nlm.nih.gov``.



Public data products

~~~~~~~~~~~~~~~~~~~~



Quebec Polyomavirus is submitted to GenBank as BK010702.



Screen of SRA metagenomes vs. RefSeq

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -83,3 +65,24 @@ The files are tab separated, with each line beginning with a RefSeq assembly acc 
  GCF_000001215.4	SRR3401361	SRR3540373

  GCF_000001405.36	SRR5127794	ERR1539652	SRR413753	ERR206081

  GCF_000001405.38	SRR5127794	ERR1539652	ERR1711677	SRR413753	ERR206081



We also provide simple scripts for searching these files: `search.tar <https://obj.umiacs.umd.edu/mash/screen/search.tar>`_



Public data sources

~~~~~~~~~~~~~~~~~~~



The BLAST ``nr`` database was downloaded from ``ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*``.



HMP data were downloaded from ``ftp://public-ftp.ihmpdcc.org/``, reads from the ``Ilumina/`` directory

and coding sequences from the ``HMGI/`` directory. Within these folders, sample SRS015937 resides in

``tongue_dorsum/`` and SRS020263 in ``right_retroauricular_crease/``.



SRA runs downloaded with the `SRA Toolkit <https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/>`_.



RefSeq genomes downloaded from the ``genomes/refseq/`` directory of ``ftp.ncbi.nlm.nih.gov``.



Public data products

~~~~~~~~~~~~~~~~~~~~



Quebec Polyomavirus is submitted to GenBank as BK010702.

doc/sphinx/index.rst

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@@ -17,6 +17,8 @@ Publication 
===========

`Mash: fast genome and metagenome distance estimation using MinHash. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x. <http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x>`_



`Mash Screen: High-throughput sequence containment estimation for genome discovery. Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM. BioRxiv. 2019 Mar. doi: 10.1101/557314 <https://doi.org/10.1101/557314>`_



.. toctree::

   :maxdepth: 1

src/mash/CommandBounds.cpp

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@@ -85,7 +85,8 @@ int CommandBounds::run() const 
				

				if ( cont )

				{

					m2j = exp(-k * dists[j]);

					//m2j = exp(-k * dists[j]);

					m2j = pow(1.0 - dists[j], k); // binomial model

				}

				else

				{
@@ -114,7 +115,8 @@ int CommandBounds::run() const 
				

				if ( cont )

				{

					j2m = -1.0 / k * log(je);

					//j2m = -1.0 / k * log(je);

					j2m = 1.0 - pow(je, 1. / k);

				}

				else

				{