YuzhenYe/TAG
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Program Name: TAG (transcript assembly by mapping reads to graphs) Version: 0.91 Released on Jan 22, 2015 Developer: Yuzhen Ye <yye@indiana.edu> and Haixu Tang <hatang@indiana.edu> Affiliation: School of Informatics and Computing, Indiana University, Bloomington The development of TAG was supported by NIH grant: NIH 1R01AI108888-01A1 TAG is free software under the terms of the GNU General Public License as published by the Free Software Foundation. >> Introduction TAG is a tool for metatranscriptome assemby by mapping metatranscriptomic reads onto graphs of matched metagenome assembly. TAG on the web: http://omics.informatics.indiana.edu/TAG (Please check the project home page for updates and newer version of the program) >> Installation go to Src/ (the source file folder), then call: make clean make The executable file "tag" will be created under the same folder >> Dependents TAG itself does not rely on any third party software; but it takes outputs from other software as its inputs. 1) SOAPdenovo2 (or SOAPdenovo); it is required for assembling matched metagenome, generating both *.contig and *.edge files. SOAPdenovo2 is available at http://sourceforge.net/projects/soapdenovo2/. 2) Bowtie2; it is required for aligning metatranscriptomic datasets onto metagenome assembly (the contig file), providing the sam file Bowtie2 is availalbe at http://bowtie-bio.sourceforge.net/bowtie2/index.shtml >> Using tag Usage: type tag for usages Inputs: metatranscriptomic sequences (strand-specific reads, in fasta format or fastq format) assembly of matched metagenome (*.contig and *.edge files) alignment of the metatranscriptomic reads onto the linear contigs in SAM format Example usage: ./tag -i T.1.fa -j T.2.fa -e G.edge -s G.contig -m S.sam -k 31 -o test-tag Inputs: T.1.fa & T.2.fa -- metatranscriptomic datasets G.edge & G.contig -- the assembly of matched metagenome (the graph file & the sequence file of the contig), produced by SOAPdenovo2 31 -- the k-mer size (NOTE: the k-mer must be same as the one used in the SOAPdenovo2 assembly!!) S.sam -- the alignment of T.1.fq & T.2.fq against G.contig, derived by Bowtie 2 Outputs: test-tag.fa -- assembled transcripts test-tag.vertex & test-tag.edge -- other outputs regarding the transcript graph (for more advanced uses, use -y option) >> Test datasets Check out datasets for testing the software at the TAG website
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