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GitHub / davidecarlson / SARS-CoV2-variant-calling-example
An educational variant calling example with short read Illumina data using the SARS-CoV2 genome
Stars: 0
Forks: 0
Open Issues: 0
License: None
Language: Python
Repo Size: 527 KB
Dependencies:
154
Created: over 3 years ago
Updated: over 3 years ago
Last pushed: over 3 years ago
Last synced: about 1 year ago
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Dependencies
environment.yaml
conda
- _libgcc_mutex 0.1
- _openmp_mutex 4.5
- _r-mutex 1.0.1
- alsa-lib 1.2.3
- bcftools 1.11
- binutils_impl_linux-64 2.35.1
- binutils_linux-64 2.35
- biopython 1.78
- bwa 0.7.17
- bwidget 1.9.14
- bzip2 1.0.8
- c-ares 1.17.1
- ca-certificates 2020.12.5
- cairo 1.16.0
- certifi 2020.12.5
- curl 7.71.1
- cycler 0.10.0
- expat 2.2.10
- fontconfig 2.13.1
- freetype 2.10.4
- fribidi 1.0.10
- gcc_impl_linux-64 9.3.0
- gcc_linux-64 9.3.0
- gdbm 1.18
- gettext 0.19.8.1
- gfortran_impl_linux-64 9.3.0
- gfortran_linux-64 9.3.0
- giflib 5.2.1
- graphite2 1.3.13
- gsl 2.6
- gxx_impl_linux-64 9.3.0
- gxx_linux-64 9.3.0
- harfbuzz 2.7.4
- hdf5 1.10.5
- htslib 1.11
- icu 68.1
- igv 2.9.0
- jpeg 9d
- kernel-headers_linux-64 2.6.32
- kiwisolver 1.3.1
- krb5 1.17.2
- lcms2 2.12
- ld_impl_linux-64 2.35.1
- libblas 3.9.0
- libcblas 3.9.0
- libcurl 7.71.1
- libdeflate 1.7
- libedit 3.1.20191231
- libev 4.33
- libffi 3.3
- libgcc-devel_linux-64 9.3.0
- libgcc-ng 9.3.0
- libgfortran-ng 9.3.0
- libgfortran5 9.3.0
- libglib 2.66.6
- libgomp 9.3.0
- libiconv 1.16
- liblapack 3.9.0
- libnghttp2 1.43.0
- libopenblas 0.3.12
- libpng 1.6.37
- libssh2 1.9.0
- libstdcxx-devel_linux-64 9.3.0
- libstdcxx-ng 9.3.0
- libtiff 4.2.0
- libuuid 2.32.1
- libwebp-base 1.2.0
- libxcb 1.13
- libxml2 2.9.10
- lz4-c 1.9.3
- make 4.3
- matplotlib 3.3.2
- matplotlib-base 3.3.2
- ncbi-ngs-sdk 2.10.9
- ncurses 6.2
- numpy 1.20.0
- olefile 0.46
- openjdk 11.0.8
- openssl 1.1.1i
- ossuuid 1.6.2
- pandas 1.2.1
- pango 1.42.4
- parallel 20201122
- patsy 0.5.1
- pcre 8.44
- pcre2 10.36
- perl 5.26.2
- perl-app-cpanminus 1.7044
- perl-business-isbn 3.004
- perl-business-isbn-data 20140910.003
- perl-carp 1.38
- perl-constant 1.33
- perl-data-dumper 2.173
- perl-encode 2.88
- perl-exporter 5.72
- perl-extutils-makemaker 7.36
- perl-file-path 2.16
- perl-file-temp 0.2304
- perl-mime-base64 3.15
- perl-parent 0.236
- perl-uri 1.76
- perl-xml-libxml 2.0132
- perl-xml-namespacesupport 1.12
- perl-xml-sax 1.02
- perl-xml-sax-base 1.09
- perl-xsloader 0.24
- picard 2.24.2
- pillow 8.1.0
- pip 21.0.1
- pixman 0.40.0
- pthread-stubs 0.4
- pyparsing 2.4.7
- python 3.8.6
- python-dateutil 2.8.1
- python_abi 3.8
- pytz 2021.1
- r-base 4.0.3
- readline 8.0
- samtools 1.11
- scipy 1.6.0
- seaborn 0.11.1
- seaborn-base 0.11.1
- sed 4.8
- setuptools 49.6.0
- six 1.15.0
- sqlite 3.34.0
- sra-tools 2.10.9
- statsmodels 0.12.2
- sysroot_linux-64 2.12
- tk 8.6.10
- tktable 2.10
- tornado 6.1
- wheel 0.36.2
- xorg-fixesproto 5.0
- xorg-inputproto 2.3.2
- xorg-kbproto 1.0.7
- xorg-libice 1.0.10
- xorg-libsm 1.2.3
- xorg-libx11 1.6.12
- xorg-libxau 1.0.9
- xorg-libxdmcp 1.1.3
- xorg-libxext 1.3.4
- xorg-libxfixes 5.0.3
- xorg-libxi 1.7.10
- xorg-libxrender 0.9.10
- xorg-libxt 1.2.1
- xorg-libxtst 1.2.3
- xorg-recordproto 1.14.2
- xorg-renderproto 0.11.1
- xorg-xextproto 7.3.0
- xorg-xproto 7.0.31
- xz 5.2.5
- zlib 1.2.11
- zstd 1.4.8