SeqSero2S: Salmonella enterica serotype prediction from genome sequencing data
Main tool : SeqSero2S
Additional tools installed via micromamba:
Name Version Build Channel
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_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.1.5 h516909a_1002 conda-forge
any2fasta 0.4.2 hdfd78af_3 bioconda
argtable2 2.13 hd590300_1004 conda-forge
bedtools 2.31.1 hf5e1c6e_2 bioconda
biopython 1.86 py312h4c3975b_0 conda-forge
blast 2.16.0 hc155240_3 bioconda
blast-legacy 2.2.26 h9ee0642_4 bioconda
bwa 0.7.18 he4a0461_1 bioconda
bzip2 1.0.8 hda65f42_8 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.10.5 hbd8a1cb_0 conda-forge
clustalo 1.2.4 h503566f_10 bioconda
clustalw 2.1 h9948957_12 bioconda
consan 1.2 h7b50bb2_7 bioconda
curl 8.8.0 he654da7_1 conda-forge
dendropy 5.0.8 pyhdfd78af_1 bioconda
dialign-tx 1.0.2 h7b50bb2_8 bioconda
dnspython 2.8.0 pyhcf101f3_0 conda-forge
entrez-direct 22.4 he881be0_0 bioconda
expat 2.7.1 hecca717_0 conda-forge
famsa 2.2.3 h9948957_1 bioconda
fasttree 2.2.0 h7b50bb2_0 bioconda
fontconfig 2.14.2 h14ed4e7_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
gawk 5.3.1 hcd3d067_0 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
gsl 2.7 he838d99_0 conda-forge
hmmer 3.4 hb6cb901_4 bioconda
htslib 1.21 h5efdd21_0 bioconda
icu 73.2 h59595ed_0 conda-forge
importlib-metadata 8.7.0 pyhe01879c_1 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
kalign2 2.04 h7b50bb2_8 bioconda
keyutils 1.6.3 hb9d3cd8_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.44 ha97dd6f_2 conda-forge
libasprintf 0.25.1 h3f43e3d_1 conda-forge
libblas 3.9.0 38_h4a7cf45_openblas conda-forge
libcblas 3.9.0 38_h0358290_openblas conda-forge
libcurl 8.8.0 hca28451_1 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
libdeflate 1.24 h86f0d12_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.1 hecca717_0 conda-forge
libffi 3.5.2 h9ec8514_0 conda-forge
libgcc 15.2.0 h767d61c_7 conda-forge
libgcc-ng 15.2.0 h69a702a_7 conda-forge
libgettextpo 0.25.1 h3f43e3d_1 conda-forge
libgfortran 15.2.0 h69a702a_7 conda-forge
libgfortran-ng 15.2.0 h69a702a_7 conda-forge
libgfortran5 15.2.0 hcd61629_7 conda-forge
libgomp 15.2.0 h767d61c_7 conda-forge
libiconv 1.18 h3b78370_2 conda-forge
libidn2 2.3.8 hfac485b_1 conda-forge
liblapack 3.9.0 38_h47877c9_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
liblzma-devel 5.8.1 hb9d3cd8_2 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_3 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 15.2.0 h8f9b012_7 conda-forge
libstdcxx-ng 15.2.0 h4852527_7 conda-forge
libtiff 4.2.0 hf544144_3 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.41.2 he9a06e4_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
libxml2 2.12.7 hc051c1a_1 conda-forge
libxslt 1.1.39 h76b75d6_0 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
lxml 5.2.2 py312hb90d8a5_0 conda-forge
mafft 7.526 h4bc722e_0 conda-forge
mlst 2.22.1 hdfd78af_0 bioconda
mpfr 4.2.1 h90cbb55_3 conda-forge
mpi 1.0 openmpi conda-forge
muscle 3.8.1551 h9948957_9 bioconda
mustang 3.2.4 h9948957_0 bioconda
ncbi-vdb 3.2.1 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.3.4 py312h33ff503_0 conda-forge
openjdk 11.0.1 h600c080_1018 conda-forge
openmpi 4.1.6 hc5af2df_101 conda-forge
openssl 3.5.4 h26f9b46_0 conda-forge
packaging 25.0 pyh29332c3_1 conda-forge
paml 4.10.9 h7b50bb2_1 bioconda
pasta 1.9.2 py312hccd54bf_5 bioconda
pcre 8.45 h9c3ff4c_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-algorithm-diff 1.201 pl5321hd8ed1ab_0 conda-forge
perl-archive-tar 3.04 pl5321hdfd78af_0 bioconda
perl-b-cow 0.007 pl5321hb9d3cd8_1 conda-forge
perl-base 2.23 pl5321hd8ed1ab_0 conda-forge
perl-bio-asn1-entrezgene 1.73 pl5321hdfd78af_3 bioconda
perl-bio-coordinate 1.007001 pl5321hdfd78af_3 bioconda
perl-bio-featureio 1.6.905 pl5321hdfd78af_4 bioconda
perl-bio-samtools 1.43 pl5321he4a0461_4 bioconda
perl-bio-searchio-hmmer 1.7.3 pl5321hdfd78af_0 bioconda
perl-bio-tools-phylo-paml 1.7.3 pl5321hdfd78af_3 bioconda
perl-bio-tools-run-alignment-clustalw 1.7.4 pl5321hdfd78af_3 bioconda
perl-bio-tools-run-alignment-tcoffee 1.7.4 pl5321hdfd78af_5 bioconda
perl-bioperl 1.7.8 hdfd78af_1 bioconda
perl-bioperl-core 1.7.8 pl5321hdfd78af_1 bioconda
perl-bioperl-run 1.007003 pl5321hdfd78af_0 bioconda
perl-business-isbn 3.007 pl5321hd8ed1ab_0 conda-forge
perl-business-isbn-data 20210112.006 pl5321hd8ed1ab_0 conda-forge
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-class-data-inheritable 0.09 pl5321ha770c72_0 conda-forge
perl-class-method-modifiers 2.13 pl5321ha770c72_0 conda-forge
perl-clone 0.46 pl5321hb9d3cd8_1 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.214 pl5321hda65f42_0 conda-forge
perl-compress-raw-zlib 2.214 pl5321h4dac143_0 conda-forge
perl-constant 1.33 pl5321hd8ed1ab_0 conda-forge
perl-data-dump 1.25 pl5321h7b50bb2_2 bioconda
perl-data-dumper 2.183 pl5321hb9d3cd8_1 conda-forge
perl-db_file 1.858 pl5321hb9d3cd8_0 conda-forge
perl-devel-stacktrace 2.04 pl5321h296ab09_0 conda-forge
perl-digest-hmac 1.05 pl5321hdfd78af_0 bioconda
perl-digest-md5 2.59 pl5321hb9d3cd8_3 conda-forge
perl-encode 3.21 pl5321hb9d3cd8_1 conda-forge
perl-encode-locale 1.05 pl5321hdfd78af_7 bioconda
perl-exception-class 1.45 pl5321ha770c72_0 conda-forge
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge
perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge
perl-file-listing 6.16 pl5321hdfd78af_0 bioconda
perl-file-slurper 0.014 pl5321hdfd78af_0 bioconda
perl-file-sort 1.01 pl5321hdfd78af_3 bioconda
perl-file-spec 3.48_01 pl5321hdfd78af_2 bioconda
perl-getopt-long 2.58 pl5321hdfd78af_0 bioconda
perl-html-parser 3.81 pl5321h4ac6f70_1 bioconda
perl-html-tagset 3.24 pl5321hdfd78af_0 bioconda
perl-http-cookiejar-lwp 0.014 pl5321hdfd78af_0 bioconda
perl-http-cookies 6.11 pl5321hdfd78af_0 bioconda
perl-http-daemon 6.16 pl5321hdfd78af_0 bioconda
perl-http-date 6.06 pl5321hdfd78af_0 bioconda
perl-http-message 7.01 pl5321hdfd78af_0 bioconda
perl-http-negotiate 6.01 pl5321hdfd78af_4 bioconda
perl-inc-latest 0.500 pl5321ha770c72_0 conda-forge
perl-io-compress 2.213 pl5321h503566f_0 bioconda
perl-io-html 1.004 pl5321hdfd78af_0 bioconda
perl-io-socket-ssl 2.075 pl5321hd8ed1ab_0 conda-forge
perl-io-string 1.08 pl5321hdfd78af_4 bioconda
perl-io-tty 1.20 pl5321hb9d3cd8_3 conda-forge
perl-io-zlib 1.15 pl5321hdfd78af_1 bioconda
perl-ipc-run 20250809.0 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_1 bioconda
perl-json-xs 4.04 pl5321h9948957_0 bioconda
perl-libwww-perl 6.81 pl5321hdfd78af_0 bioconda
perl-libxml-perl 0.08 pl5321hdfd78af_3 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h7b50bb2_5 bioconda
perl-lwp-mediatypes 6.04 pl5321hdfd78af_1 bioconda
perl-lwp-protocol-https 6.14 pl5321hdfd78af_1 bioconda
perl-mime-base64 3.16 pl5321hb9d3cd8_3 conda-forge
perl-module-build 0.4234 pl5321ha770c72_1 conda-forge
perl-module-load 0.34 pl5321hdfd78af_0 bioconda
perl-moo 2.005004 pl5321ha770c72_0 conda-forge
perl-mozilla-ca 20250602 pl5321hdfd78af_0 bioconda
perl-net-http 6.24 pl5321hdfd78af_0 bioconda
perl-net-ssleay 1.92 pl5321hf14f497_1 conda-forge
perl-ntlm 1.09 pl5321hdfd78af_5 bioconda
perl-parent 0.243 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321hb9d3cd8_2 conda-forge
perl-role-tiny 2.002004 pl5321ha770c72_0 conda-forge
perl-scalar-list-utils 1.70 pl5321hb03c661_0 conda-forge
perl-socket 2.027 pl5321h5c03b87_6 bioconda
perl-storable 3.15 pl5321hb9d3cd8_2 conda-forge
perl-sub-quote 2.006006 pl5321ha770c72_0 conda-forge
perl-sub-uplevel 0.2800 pl5321hb9d3cd8_0 conda-forge
perl-test-deep 1.130 pl5321hd8ed1ab_0 conda-forge
perl-test-differences 0.72 pl5321ha770c72_0 conda-forge
perl-test-exception 0.43 pl5321hd8ed1ab_0 conda-forge
perl-test-fatal 0.016 pl5321ha770c72_0 conda-forge
perl-test-most 0.38 pl5321hdfd78af_0 bioconda
perl-test-needs 0.002009 pl5321hd8ed1ab_0 conda-forge
perl-test-requiresinternet 0.05 pl5321hdfd78af_1 bioconda
perl-test-warn 0.37 pl5321hd8ed1ab_0 conda-forge
perl-test-warnings 0.031 pl5321ha770c72_0 conda-forge
perl-text-diff 1.45 pl5321hd8ed1ab_0 conda-forge
perl-time-local 1.35 pl5321hdfd78af_0 bioconda
perl-timedate 2.33 pl5321hdfd78af_2 bioconda
perl-tree-dag_node 1.35 pl5321hdfd78af_0 bioconda
perl-try-tiny 0.31 pl5321ha770c72_0 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
perl-uri 5.34 pl5321ha770c72_0 conda-forge
perl-url-encode 0.03 pl5321h9ee0642_1 bioconda
perl-www-robotrules 6.02 pl5321hdfd78af_4 bioconda
perl-xml-dom 1.46 pl5321hdfd78af_1 bioconda
perl-xml-dom-xpath 0.14 pl5321hdfd78af_2 bioconda
perl-xml-parser 2.44_01 pl5321hf2e2c51_1004 conda-forge
perl-xml-regexp 0.04 pl5321hdfd78af_3 bioconda
perl-xml-xpathengine 0.14 pl5321hdfd78af_3 bioconda
phylip 3.697 h7b50bb2_3 bioconda
pip 25.2 pyh8b19718_0 conda-forge
poa 2.0 h7b50bb2_6 bioconda
prank 170427 h9948957_1 bioconda
probcons 1.12 h8b12597_1 bioconda
probconsrna 1.10 h9f5acd7_4 bioconda
proda 1.0 h503566f_7 bioconda
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pyfaidx 0.9.0.3 pyhdfd78af_0 bioconda
pymongo 4.15.3 py312h1289d80_0 conda-forge
python 3.12.3 hab00c5b_0_cpython conda-forge
python_abi 3.12 8_cp312 conda-forge
pyvcf3 1.0.4 py312h0fa9677_0 bioconda
raxml 8.2.13 h7b50bb2_3 bioconda
readline 8.2 h8c095d6_2 conda-forge
rpsbproc 0.5.0 h6a68c12_1 bioconda
salmid 0.1.23 py_0 bioconda
samtools 1.21 h50ea8bc_0 bioconda
sap 1.1.3 h7b50bb2_5 bioconda
seqsero2s 1.1.4 pyhdfd78af_0 bioconda
seqtk 1.4 he4a0461_2 bioconda
setuptools 80.9.0 pyhff2d567_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
sniffio 1.3.1 pyhd8ed1ab_1 conda-forge
spades 4.0.0 h6dccd9a_3 bioconda
sra-tools 2.9.6 hf484d3e_0 bioconda
stringmlst 0.6.3 py_0 bioconda
t-coffee 13.46.2.7c9e712d pl5321hb2a3317_0 bioconda
tk 8.6.13 noxft_h4845f30_101 conda-forge
tmalign 20170708 h8d36177_7 bioconda
tzdata 2025b h78e105d_0 conda-forge
viennarna 2.7.0 py312pl5321h9f0f9fd_0 bioconda
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.2 hb03c661_0 conda-forge
xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
xz 5.8.1 hbcc6ac9_2 conda-forge
xz-gpl-tools 5.8.1 hbcc6ac9_2 conda-forge
xz-tools 5.8.1 hb9d3cd8_2 conda-forge
zipp 3.23.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h4ab18f5_6 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
Please note that although the SeqSero2S.py --version command works as anticipated (output: SeqSero2S.py 1.1.4), there are two "Predicted serotype" outputs, one of which says (SeqSero2 v1.3.2). This is hardcoded in the SeqSero2S.py script.
# paired end Illumina reads as input for allele mode
$ SeqSero2S.py \
-i SRR6082043_1.fastq.gz SRR6082043_2.fastq.gz \
-t 2 \
-m a \
-d SRR6082043-seqsero2s-reads-allele-mode
-n SRR6082043 \
-p 2
/opt/conda/bin/SeqSero2S.py:1238: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(version)<=LooseVersion("1.2"):
[bam_sort_core] merging from 0 files and 2 in-memory blocks...
building database...
mapping...
check samtools version: 1.21
assembling...
blasting...
Sample name: SRR6082043
Output directory: /test/SRR6082043-seqsero2s-reads-allele-mode
Input files: /test/SRR6082043_1.fastq.gz /test/SRR6082043_2.fastq.gz
O antigen prediction: 7
H1 antigen prediction(fliC): r
H2 antigen prediction(fljB): 1,5
Predicted identification: Salmonella enterica subspecies enterica (subspecies I)
Predicted antigenic profile: 7:r:1,5
Predicted serotype: Infantis
Predicted serotype (SeqSero2 v1.3.2): Infantis
Note:
Sequence type: 32
Number of ST32 strains in EnteroBase: 19554
aroC: 17
dnaN: 18
hemD: 22
hisD: 17
purE: 5
sucA: 21
thrA: 19
Predicted serotype: Infantis
Predicted serotype (SeqSero2 v1.3.2): Infantis
# genome assembly FASTA as input for kmer mode
$ SeqSero2S.py \
-i GCA_007765495.1.genomic.fna \
-t 4 \
-m k \
-d GCA_007765495.1-seqsero2s-assembly-kmer-mode \
-n GCA_007765495.1 \
-p 2
Sample name: GCA_007765495.1
Output directory: /test/GCA_007765495.1-seqsero2-assembly-kmer-mode
Input files: GCA_007765495.1.genomic.fna
O antigen prediction: 7
H1 antigen prediction(fliC): r
H2 antigen prediction(fljB): 1,5
Predicted identification: Salmonella enterica subspecies enterica (subspecies I)
Predicted antigenic profile: 7:r:1,5
Predicted serotype: Infantis
Predicted serotype (SeqSero2 v1.3.2): Infantis
Note:
Sequence type: 32
Number of ST32 strains in EnteroBase: 19554
aroC: 17
dnaN: 18
hemD: 22
hisD: 17
purE: 5
sucA: 21
thrA: 19
Predicted serotype: Infantis
Predicted serotype (SeqSero2 v1.3.2): Infantis