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GitHub / alipirani88 / snpkit

Modular workflow for Microbial Variant Calling and SNP diagnostics.

JSON API: https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alipirani88%2Fsnpkit

Stars: 4
Forks: 4
Open Issues: 1

License: mit
Language: Python
Repo Size: 61.8 MB
Dependencies: 175

Created: over 6 years ago
Updated: 6 days ago
Last pushed: 6 days ago
Last synced: 6 days ago

Topics: bacteria, genomics, ngs, pipeline, snps, variant-calling, vcf

Files

Readme

Dependencies

envs/Dockerfile docker

ubuntu 18.04 build

misc/Dockerfile docker

ubuntu 18.04 build

envs/environment.yml conda

_libgcc_mutex 0.1
_openmp_mutex 4.5
_r-mutex 1.0.1
alsa-lib 1.2.7.2
bcftools 1.2
bedtools 2.30.0
binutils_impl_linux-64 2.39
bioawk 1.0
blas 1.0
bwa 0.7.17
bwidget 1.9.14
bzip2 1.0.8
c-ares 1.18.1
ca-certificates 2022.07.19
cairo 1.16.0
curl 7.85.0
dbus 1.13.18
expat 2.4.9
font-ttf-dejavu-sans-mono 2.37
font-ttf-inconsolata 3.000
font-ttf-source-code-pro 2.038
font-ttf-ubuntu 0.83
fontconfig 2.14.0
fonts-conda-ecosystem 1
fonts-conda-forge 1
freetype 2.12.1
fribidi 1.0.10
gatk 3.8
gatk4 4.3.0.0
gcc_impl_linux-64 12.2.0
gettext 0.21.1
gfortran_impl_linux-64 12.2.0
giflib 5.2.1
glib 2.74.0
glib-tools 2.74.0
graphite2 1.3.14
gsl 2.7.1
gxx_impl_linux-64 12.2.0
harfbuzz 5.3.0
htslib 1.9
icu 70.1
jpeg 9e
kernel-headers_linux-64 2.6.32
keyutils 1.6.1
krb5 1.19.3
lcms2 2.12
ld_impl_linux-64 2.39
lerc 4.0.0
libblas 3.9.0
libcblas 3.9.0
libcups 2.3.3
libcurl 7.85.0
libdeflate 1.14
libedit 3.1.20210910
libev 4.33
libffi 3.4.2
libgcc 7.2.0
libgcc-devel_linux-64 12.2.0
libgcc-ng 12.2.0
libgfortran-ng 12.2.0
libgfortran5 12.2.0
libglib 2.74.0
libgomp 12.2.0
libiconv 1.17
liblapack 3.9.0
libnghttp2 1.47.0
libnsl 2.0.0
libopenblas 0.3.21
libpng 1.6.38
libsanitizer 12.2.0
libsqlite 3.39.4
libssh2 1.10.0
libstdcxx-devel_linux-64 12.2.0
libstdcxx-ng 12.2.0
libtiff 4.4.0
libuuid 2.32.1
libwebp-base 1.2.4
libxcb 1.15
libxml2 2.10.3
libzlib 1.2.13
make 4.3
mash 1.1
mummer 3.23
ncurses 6.3
openjdk 8.0.152
openssl 3.0.5
packaging 21.3
pango 1.50.11
pcre2 10.37
perl 5.32.1
picard 2.27.4
pip 22.3
pixman 0.40.0
pyfasta 0.5.2
python 3.10.6
python-dateutil 2.8.2
python_abi 3.10
r-base 4.2.1
r-bitops 1.0_7
r-catools 1.18.2
r-cli 3.3.0
r-colorspace 2.0_3
r-crayon 1.5.1
r-digest 0.6.29
r-ellipsis 0.3.2
r-fansi 1.0.3
r-farver 2.1.0
r-ggplot2 3.3.6
r-glue 1.6.2
r-gplots 3.1.3
r-gsalib 2.1
r-gtable 0.3.0
r-gtools 3.9.2.1
r-isoband 0.2.5
r-kernsmooth 2.23_20
r-labeling 0.4.2
r-lattice 0.20_45
r-lifecycle 1.0.1
r-magrittr 2.0.3
r-mass 7.3_57
r-matrix 1.4_1
r-mgcv 1.8_40
r-munsell 0.5.0
r-nlme 3.1_157
r-pillar 1.7.0
r-pkgconfig 2.0.3
r-plyr 1.8.7
r-r6 2.5.1
r-rcolorbrewer 1.1_3
r-rcpp 1.0.8.3
r-reshape 0.8.9
r-rlang 1.0.2
r-scales 1.2.0
r-tibble 3.1.7
r-utf8 1.2.2
r-vctrs 0.4.1
r-viridislite 0.4.0
r-withr 2.5.0
readline 8.1.2
samclip 0.4.0
samtools 1.2
sed 4.8
seqtk 1.3
setuptools 65.5.0
six 1.16.0
snpeff 4.3.1t
sysroot_linux-64 2.12
tabix 1.11
tk 8.6.12
tktable 2.10
trimmomatic 0.39
tzdata 2022e
vcftools 0.1.16
wheel 0.37.1
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 1.7.2
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 5.2.6
zlib 1.2.13
zstd 1.5.2