Edit README md

README.md

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 Introduction:
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 Lineanator uses USEARCH and NCBI to create a database file with confidences up to the species level. 
 This database file can be used in MC-SMRT to assign taxonomy and confidences to OTUs in a microbiome community.
 
 
 Installation and Dependencies: 
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 1) Ruby gems such as bio, troloop and nokogiri are required for Lineanator to function. Use the "gem install {name_of_the_gem}" command to install these gems.
 2) Download and install usearch v8.1.
    Create a soft link pointing towards this version of usearch and name it "usearch". The soft link name HAS TO BE usearch, this is VERY IMPORTANT.
 
 
 Usage: 
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 ruby lineanator.rb [-h] [-d DUMP_FILE] [-s SEQ_FILE] [-t TAB_DELIMITED_LINEAGE_OUTPUT_FILE] [-f FASTA_LINEAGE_OUTPUT_FILE] [-p PLACE_HOLDER_NAMES_FILE]
 
 
 Arguments explained:
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 1) DUMP_FILE - This text file serves as a source to map between the gi id's in the SEQ_FILE and get the tax id's corresponding to each gi id. 
    The dump file we used was taken from NCBI's taxonomy FTP (ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/). 
    The directory called gi_taxid_nucl.zip in the FTP had a file with gi id in the first column and tax id in the second column (no headers).
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 Output files:
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 Two of the output files are the ones which you gave as arguments to lineanator, these are expalined above.
 
 The basename of the FASTA_LINEAGE_OUTPUT_FILE given by you is used for creating other files using USEARCH commands. 
@@ -43,4 +48,5 @@ For example, if the name of your FASTA_LINEAGE_OUTPUT_FILE is "16sMicrobial_ncbi
 
 
 Built with: 
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 ruby 2.2.1p85 (2015-02-26 revision 49769) [x86_64-linux]