Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
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M. Hess, A. Sczyrba, R. Egan, T.-W. Kim, H. Chokhawala, G. Schroth, S. Luo, 
D.S. Clark, F. Chen, T. Zhang, R.I. Mackie, L.A. Pennacchio, S.G. Tringe,
A. Visel, T. Woyke, Z. Wang, and E.M. Rubin

http://www.sciencemag.org/content/331/6016/463.abstract

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Raw data:
=========
rumen libraries

####
INSERT:		5kb
SOURCE:		JGI
TITRATION:	GTNH    I5kT.741.[45].920.fq 
SEQUENCES:	GTOB    I5k.756.[1-7].948.fq

####
INSERT:		3kb
SOURCE:		JGI
TITRATION:	GTNI    I3kT.741.[67].920.fq
SEQUENCES:	GTOC    I3k.811.[1-7].1014.fq

####
INSERT:		200bp
SOURCE:		ILLUMINA
TITRATION:	NONE
SEQUENCES:	I200_s_[1-8].fq

####
INSERT:		300bp
SOURCE:		ILLUMINA
PLATFORM:	HiSeq
SEQUENCES:	I300HFC[AB]_s_[1-8].fq

SOURCE:		JGI
TITRATION: 	HWN[ST] I300T.877.[1-4].1049.fq


Scaffolds of velvet assemblies
==============================
cow_rumen_initial_velvet_assembly_scaffolds.fas.gz
cow_rumen_fragmented_velvet_assembly_scaffolds.fas.gz

Initial velvet scaffolds were only used for gene prediction. The
scaffolds generated from the velvet assembly were aligned, using
bowtie, against the set of artifact filtered sequences. Based on the
alignment information, the scaffolds were subsequently broken into
separate regions. See supporting online material at
http://www.sciencemag.org/content/331/6016/463.abstract for details.
After fragmenting the scaffolds at the break points, only scaffolds
that are larger than 10kb (total 26,042) were kept for further
analysis (genome binning).


Metagenemark gene predictions
=============================
Protein sequences:    metagenemark_predictions.faa.gz
Nucleotide sequences: metagenemark_predictions.fna.gz


Genome Bins
===========
cow_rumen_genome_bins.tar.gz