Main tool: GenoFLU
Code repository: https://github.com/USDA-VS/GenoFLU
Additional tools installed via micromamba:
List of packages in environment: "/opt/conda"
Name Version Build Channel
────────────────────────────────────────────────────────────────────────────
_openmp_mutex 4.5 20_gnu conda-forge
biopython 1.86 py314h5bd0f2a_1 conda-forge
blast 2.17.0 h66d330f_0 bioconda
bzip2 1.0.8 hda65f42_9 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
ca-certificates 2026.2.25 hbd8a1cb_0 conda-forge
curl 8.18.0 hcf29cc6_1 conda-forge
entrez-direct 24.0 he881be0_0 bioconda
et_xmlfile 2.0.0 pyhd8ed1ab_1 conda-forge
genoflu 1.07 hdfd78af_0 bioconda
icu 78.2 h33c6efd_0 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
krb5 1.22.2 ha1258a1_0 conda-forge
ld_impl_linux-64 2.45.1 default_hbd61a6d_101 conda-forge
libblas 3.11.0 5_h4a7cf45_openblas conda-forge
libcblas 3.11.0 5_h0358290_openblas conda-forge
libcurl 8.18.0 hcf29cc6_1 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.4 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libgcc 15.2.0 he0feb66_18 conda-forge
libgcc-ng 15.2.0 h69a702a_18 conda-forge
libgfortran 15.2.0 h69a702a_18 conda-forge
libgfortran5 15.2.0 h68bc16d_18 conda-forge
libgomp 15.2.0 he0feb66_18 conda-forge
libidn2 2.3.8 hfac485b_1 conda-forge
liblapack 3.11.0 5_h47877c9_openblas conda-forge
liblzma 5.8.2 hb03c661_0 conda-forge
libmpdec 4.0.0 hb03c661_1 conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libsqlite 3.51.2 hf4e2dac_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_18 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
ncbi-vdb 3.3.0 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
numpy 2.4.2 py314h2b28147_1 conda-forge
openpyxl 3.1.5 py314hf3b76af_3 conda-forge
openssl 3.6.1 h35e630c_1 conda-forge
pandas 3.0.1 py314hb4ffadd_0 conda-forge
pcre2 10.47 haa7fec5_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-archive-tar 3.04 pl5321hdfd78af_0 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 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-encode 3.21 pl5321hb9d3cd8_1 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-io-compress 2.216 pl5321h503566f_0 bioconda
perl-io-zlib 1.15 pl5321hdfd78af_1 bioconda
perl-json 4.10 pl5321hdfd78af_1 bioconda
perl-json-xs 4.04 pl5321h9948957_0 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h7b50bb2_5 bioconda
perl-parent 0.243 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321hb9d3cd8_2 conda-forge
perl-scalar-list-utils 1.70 pl5321hb03c661_0 conda-forge
perl-storable 3.15 pl5321hb9d3cd8_2 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
pip 26.0.1 pyh145f28c_0 conda-forge
python 3.14.3 h32b2ec7_101_cp314 conda-forge
python-dateutil 2.9.0.post0 pyhe01879c_2 conda-forge
python_abi 3.14 8_cp314 conda-forge
readline 8.3 h853b02a_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
tk 8.6.13 noxft_h366c992_103 conda-forge
tzdata 2025c hc9c84f9_1 conda-forge
wget 1.25.0 h653f8fd_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
Basic information on how to use this tool:
- executable:
genoflu.py - help:
--help - version:
--version - description: "GenoFLU determines the genotype of a segmented flu sample by BLASTing a multi-segment FASTA against the BLAST database"
Additional information:
Full documentation: https://github.com/USDA-VS/GenoFLU
genoflu.py -f input.fasta