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German Uritskiy
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metaWRAP v=0.4
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‎README.md‎

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# metaWRAP - Comprehensive Metagenome Analysis in One Place
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## metaWRAP version 0.4
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## metaWRAP v=0.4
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metaWRAP aims to be an easy-to-use inclusive wrapper program that accomplishes the most basic tasks in metagenomic analysis: QC, assembly, binning, visualization, and taxonomic profiling. While there is no single best approach for processing metagenomic data, metaWRAP is meant to be a fast and simple first pass program before you delve deeper into parameterization of your approach. Each individual component of the pipeline is also a standalone module. This modularity allows the users to use only the modules they are interested in.
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‎dependancies.txt‎

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#ALL DEPENDANCIES:
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-BLAST 2.6.0+
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-bmtagger 3.101
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-Bowtie2 2.3.2
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-bwa 0.7.15-r1140
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-Checkm v1.0.7
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-FastQC v0.11.5
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-kraken 0.10.6
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-kronatools 2.7
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-megahit v1.1.1-2-g02102e1
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-metabat2 2.9.1
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-concoct 0.4.0
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-MaxBin2 2.2.4
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-perl v5.22.0
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-python2.7
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-quast v4.5
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-R 3.3.2
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-ggplot2
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-samtools 1.3.1
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-SPAdes v3.10.1
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-trim_galore 0.4.3
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-python 2.7
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-seaborn 0.8.1
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-salmon
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-matplotlib
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#DATABASES:
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1.4GB Checkm_DB (past of CheckM installation)
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161GB -KRAKEN standard database
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71GB RefSeq NCBI_nt
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283MB RefSeq NCBI_tax
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20GB Indexed hg38 (for bmtagger)
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#More detailed dependancies:
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general:
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-python2.7
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read_qc.sh
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-fastqc v0.11.5
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-trim_galore 0.4.3
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-bmtagger 3.101
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-human_db hg38
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assembly.sh
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-SPAdes v3.10.1
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-bwa 0.7.15-r1140
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-megahit v1.1.1-2-g02102e1
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-quast v4.5
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binning.sh
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-bwa 0.7.15-r1140
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-samtools 1.3.1
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-metabat2 2.9.1
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-concoct 0.4.0
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-MaxBin2 2.2.4
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bin_refinement.sh
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-python 2.7
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-matplotlib
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-checkm v1.0.7
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-checkm_DB (standard)
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reassemble_bins.sh
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-bwa 0.7.15-r1140
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-samtools 1.3.1
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-checkm v1.0.7
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-checkm_DB (standard)
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-SPAdes 3.11.1
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quant_bins.sh
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-salmon
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-seaborn 0.8.1
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blobology.sh
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-refseq_db NCBI_nt
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-refseq_db NCBI_tax
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-blast 2.6.0+
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-bowtie2 2.3.2
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-perl v5.22.0
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-R 3.3.2
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-ggplot2
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kraken.sh
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-kraken 0.10.6
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-kraken_db STANDARD_DATABASE
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-kronatools 2.7
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‎environment.yml‎

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name: metawrap
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channels:
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- bioconda
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- r
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- defaults
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- conda-forge
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dependencies:
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- bcftools=1.3.1=1
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- biopython=1.69=np110py27_0
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- blast=2.7.1=boost1.64_1
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- bmfilter=3.101=1
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- bmtagger=3.101=3
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- bmtool=3.101=1
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- bowtie2=2.3.0=py27_1
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- bwa=0.7.15=1
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- checkm-genome=1.0.7=py27_0
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- concoct=0.4.0=gsl1.16_0
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- cutadapt=1.15=py27_0
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- dendropy=4.2.0=py27_0
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- extract_fullseq=3.101=2
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- fastqc=0.11.5=1
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- ggplot=0.6.8=py27_0
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- htslib=1.3=0
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- java-jdk=8.0.92=1
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- jemalloc=4.5.0=0
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- kraken=0.10.6_eaf8fb68=2
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- megahit=1.1.2=py27_0
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- mmtf-python=1.0.2=py27_0
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- perl-threaded=5.22.0=10
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- pysam=0.9.0=py27_1
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- python-dateutil=2.3=py27_0
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- quast=4.1=py27_0
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- salmon=0.9.1=0
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- samtools=1.6=0
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- screamingbackpack=0.2.333=py27_0
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- simplejson=3.8.1=py27_0
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- srprism=2.4.24=2
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- tbb=4.4_20150728=0
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- trim-galore=0.4.5=pl5.22.0_0
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- typing=3.5.2.2=py27_0
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- xopen=0.3.2=py27_0
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- boost=1.64.0=py27_4
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- boost-cpp=1.64.0=1
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- brewer2mpl=1.4.1=py27_2
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- gnutls=3.5.15=0
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- gsl=1.16=0
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- libidn11=1.33=0
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- nettle=3.3=0
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- perl=5.22.0.1=0
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- pyqt=4.11.4=py27_2
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- alabaster=0.7.10=py27he5a193a_0
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- asn1crypto=0.23.0=py27h7b0c810_0
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- babel=2.5.0=py27h20693cd_0
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- backports=1.0=py27h63c9359_1
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- backports_abc=0.5=py27h7b3c97b_0
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- bz2file=0.98=py27_0
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- bzip2=1.0.6=h6d464ef_2
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- ca-certificates=2017.08.26=h1d4fec5_0
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- cairo=1.14.8=0
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- certifi=2017.11.5=py27h71e7faf_0
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- cffi=1.11.2=py27ha7929c6_0
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- chardet=3.0.4=py27hfa10054_1
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- cryptography=2.1.4=py27h6697b16_0
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- curl=7.52.1=0
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- cycler=0.10.0=py27hc7354d3_0
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- cython=0.27.3=py27hc56b35e_0
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- docutils=0.14=py27hae222c1_0
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- enum34=1.1.6=py27h99a27e9_1
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- fontconfig=2.12.1=3
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- freetype=2.5.5=2
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- functools32=3.2.3.2=py27h4ead58f_1
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- gmp=6.1.2=h6c8ec71_1
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- icu=58.2=h9c2bf20_1
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- idna=2.6=py27h5722d68_1
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- imagesize=0.7.1=py27hd17bf80_0
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- intel-openmp=2018.0.0=hc7b2577_8
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- ipaddress=1.0.18=py27h337fd85_0
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- jinja2=2.10=py27h4114e70_0
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- joblib=0.11=py27_0
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- libedit=3.1=heed3624_0
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- libffi=3.2.1=hd88cf55_4
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- libgcc=7.2.0=h69d50b8_2
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- libgcc-ng=7.2.0=h7cc24e2_2
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- libgfortran=3.0.0=1
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- libgfortran-ng=7.2.0=h9f7466a_2
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- libiconv=1.14=0
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- libpng=1.6.30=1
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- libstdcxx-ng=7.2.0=h7a57d05_2
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- libxml2=2.9.4=0
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- markupsafe=1.0=py27h97b2822_1
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- matplotlib=1.5.1=np110py27_0
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- mkl=2018.0.1=h19d6760_4
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- msgpack-python=0.4.8=py27hc2fa789_0
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- ncurses=6.0=h9df7e31_2
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- nose=1.3.7=py27heec2199_2
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- numpy=1.10.2=py27_0
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- openblas=0.2.14=4
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- openssl=1.0.2m=h26d622b_1
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- pandas=0.21.0=py27he307072_1
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- patsy=0.4.1=py27hd1cf8c0_0
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- pcre=8.41=hc27e229_1
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- pip=9.0.1=py27ha730c48_4
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- pixman=0.34.0=hceecf20_3
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- pycairo=1.13.3=py27hea6d626_0
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- pycparser=2.18=py27hefa08c5_1
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- pygments=2.2.0=py27h4a8b6f5_0
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- pyopenssl=17.5.0=py27hcee3be0_0
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- pyparsing=2.2.0=py27hf1513f8_1
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- pysocks=1.6.7=py27he2db6d2_1
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- python=2.7.11=0
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- pytz=2017.3=py27h001bace_0
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- qt=4.8.5=0
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- readline=6.2=2
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- reportlab=3.2.0=py27_0
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- requests=2.18.4=py27hc5b0589_1
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- scikit-learn=0.19.1=py27h445a80a_0
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- scipy=1.0.0=py27hf5f0f52_0
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- seaborn=0.8.1=py27h633ea1e_0
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- setuptools=36.5.0=py27h68b189e_0
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- singledispatch=3.4.0.3=py27h9bcb476_0
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- sip=4.18=py27_0
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- six=1.11.0=py27h5f960f1_1
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- snowballstemmer=1.2.1=py27h44e2768_0
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- sphinx=1.6.3=py27hf9b1778_0
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- sphinx_rtd_theme=0.2.4=py27_0
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- sphinxcontrib=1.0=py27h1512b58_1
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- sphinxcontrib-websupport=1.0.1=py27hf906f22_1
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- sqlite=3.20.1=hb898158_2
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- ssl_match_hostname=3.5.0.1=py27h4ec10b9_2
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- statsmodels=0.8.0=py27hc87d62d_0
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- subprocess32=3.2.7=py27h373dbce_0
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- tk=8.5.18=0
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- tornado=4.5.2=py27h97b179f_0
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- urllib3=1.22=py27ha55213b_0
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- wheel=0.30.0=py27h2bc6bb2_1
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- xz=5.2.3=h55aa19d_2
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- zlib=1.2.8=3
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- pip:
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- backports-abc==0.5
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- backports.ssl-match-hostname==3.5.0.1
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- sphinx-rtd-theme==0.2.4
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prefix: /home/guritsk1/miniconda2/envs/metawrap
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