PhyloSift – More test data and Devel continuation

Other Shotgun Metagenomes for HMP studies

We needed to get some PE-Illumina HiSeq data, since it looks like the HMP mock communities are only GAIIx single-end data. File sizes for Hiseq data are waaaay bigger though, so I’m starting off with just one SRA dataset:

http://www.ncbi.nlm.nih.gov/sra/SRX025948

wget ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByExp/litesra/SRX/SRX025/SRX025948/SRR064531/SRR064531.lite.sra

To unpack SRA files, I’ve been running the following command for the toolkit on Edhar:

/home/koadman/software/sratoolkit.2.1.10-ubuntu32/bin/fastq-dump –split-spot SRR064531.lite.sra

Devel branch progress

After running into issues yesterday, I waited for devel to re-build overnight and downloaded the new version this morning. Need to specify the devel marker path by using the command as follows:

./phylosift.pl all -marker_url=”http://edhar.genomecenter.ucdavis.edu/~koadman/phylosift_markers/devel” /home/hollybik/TestData/xeno_assembly_low_cov_NameEdit.fa

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