Main tool: seroba
Code repository: https://github.com/GlobalPneumoSeq/seroba
Additional tools installed via micromamba:
Name Version Build Channel
─────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
ariba 2.14.3 py36he1b5a44_0 bioconda
bcftools 1.9 h68d8f2e_9 bioconda
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
biopython 1.79 py36h8f6f2f9_0 conda-forge
bowtie2 2.5.4 h7071971_4 bioconda
brotlipy 0.7.0 py36h8f6f2f9_1001 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.8.3 hbd8a1cb_0 conda-forge
cd-hit 4.8.1 h43eeafb_11 bioconda
certifi 2021.5.30 py36h5fab9bb_0 conda-forge
cffi 1.14.4 py36h211aa47_0 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
cryptography 35.0.0 py36hb60f036_0 conda-forge
curl 7.87.0 h6312ad2_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 hfdff14a_1 conda-forge
dendropy 5.0.8 pyhdfd78af_1 bioconda
expat 2.7.1 hecca717_0 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gettext 0.25.1 h3f43e3d_1 conda-forge
gettext-tools 0.25.1 h3f43e3d_1 conda-forge
glib 2.66.3 h58526e2_0 conda-forge
gsl 2.5 h294904e_1 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
htslib 1.9 h244ad75_9 bioconda
icu 64.2 he1b5a44_1 conda-forge
idna 3.10 pyhd8ed1ab_0 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
kernel-headers_linux-64 3.10.0 he073ed8_18 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
kiwisolver 1.3.1 py36h605e78d_1 conda-forge
kmc 3.2.4 h6dccd9a_2 bioconda
krb5 1.20.1 hf9c8cef_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.44 h1423503_1 conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libasprintf-devel 0.25.1 h3f43e3d_1 conda-forge
libblas 3.9.0 34_h59b9bed_openblas conda-forge
libcblas 3.9.0 34_he106b2a_openblas conda-forge
libclang 9.0.1 default_hb4e5071_5 conda-forge
libcurl 7.87.0 h6312ad2_0 conda-forge
libdeflate 1.24 h86f0d12_0 conda-forge
libedit 3.1.20191231 h46ee950_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.1 hecca717_0 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc 15.1.0 h767d61c_4 conda-forge
libgcc-ng 15.1.0 h69a702a_4 conda-forge
libgettextpo 0.25.1 h3f43e3d_1 conda-forge
libgettextpo-devel 0.25.1 h3f43e3d_1 conda-forge
libgfortran 15.1.0 h69a702a_4 conda-forge
libgfortran5 15.1.0 hcea5267_4 conda-forge
libglib 2.66.3 hbe7bbb4_0 conda-forge
libgomp 15.1.0 h767d61c_4 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libidn2 2.3.8 ha4ef2c3_0 conda-forge
liblapack 3.9.0 34_h7ac8fdf_openblas conda-forge
libllvm9 9.0.1 default_hc23dcda_7 conda-forge
libnghttp2 1.51.0 hdcd2b5c_0 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_2 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx 15.1.0 h8f9b012_4 conda-forge
libstdcxx-ng 15.1.0 h4852527_4 conda-forge
libtiff 4.2.0 hf544144_3 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.6.0 hd42ef1d_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 0.10.0 he1b5a44_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
llvm-openmp 8.0.1 hc9558a2_0 conda-forge
matplotlib 3.3.4 py36h5fab9bb_0 conda-forge
matplotlib-base 3.3.4 py36hd391965_0 conda-forge
mummer 3.23 pl5321h503566f_21 bioconda
ncurses 6.1 hf484d3e_1002 conda-forge
nspr 4.37 h29cc59b_0 conda-forge
nss 3.100 hca3bf56_0 conda-forge
numpy 1.19.5 py36hfc0c790_2 conda-forge
olefile 0.46 pyh9f0ad1d_1 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openmp 8.0.1 0 conda-forge
openssl 1.1.1w hd590300_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pillow 8.2.0 py36ha6010c0_1 conda-forge
pip 21.3.1 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyfastaq 3.17.0 py_2 bioconda
pymummer 0.10.3 py_2 bioconda
pyopenssl 22.0.0 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.4 pyhd8ed1ab_0 conda-forge
pyqt 5.12.3 py36haa643ae_3 conda-forge
pysam 0.15.0.1 py36hdfb72b2_1 bioconda
pysocks 1.7.1 py36h5fab9bb_3 conda-forge
python 3.6.10 h8356626_1011_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.6 2_cp36m conda-forge
pyyaml 5.4.1 py36h8f6f2f9_1 conda-forge
qt 5.12.5 hd8c4c69_1 conda-forge
readline 8.0 h46ee950_1 conda-forge
requests 2.28.1 pyhd8ed1ab_0 conda-forge
samtools 1.9 h10a08f8_12 bioconda
setuptools 58.0.4 py36h5fab9bb_2 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
spades 3.15.5 h95f258a_1 bioconda
sqlite 3.32.3 hcee41ef_1 conda-forge
sysroot_linux-64 2.17 h0157908_18 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tornado 6.1 py36h8f6f2f9_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
urllib3 1.26.15 pyhd8ed1ab_0 conda-forge
wget 1.20.3 ha56f1ee_1 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h280c20c_3 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Basic information on how to use this tool:
- executable:
seroba - help:
-h,--help - version:
version - description: SeroBA is a k-mer based Pipeline to identify the Serotype from Illumina NGS reads for given references.
Additional information:
- This image contains 71-mer database at
/seroba/database/
Full documentation: https://sanger-pathogens.github.io/seroba/
# Create a database for kmc and ariba
seroba createDBs <database dir> <kmer size>
# Identify serotype
seroba runSerotyping [options] <databases directory> <read1> <read2> <prefix>
# Summarize the output in one tsv file
seroba summary <output folder>