Main tool: plassembler
Code repository: https://github.com/gbouras13/plassembler
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
about-time 4.2.1 pyhd8ed1ab_0 conda-forge
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blast 2.16.0 h66d330f_4 bioconda
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certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
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curl 8.12.1 h332b0f4_0 conda-forge
cyrus-sasl 2.1.27 h54b06d7_7 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
dnaapler 0.8.1 pyhdfd78af_0 bioconda
entrez-direct 22.4 he881be0_0 bioconda
expat 2.6.4 h5888daf_0 conda-forge
fastp 0.24.0 heae3180_1 bioconda
flye 2.9.5 py38hd638cd3_1 bioconda
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fribidi 1.0.10 h36c2ea0_0 conda-forge
gettext 0.23.1 h5888daf_0 conda-forge
gettext-tools 0.23.1 h5888daf_0 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
glib 2.82.2 h07242d1_1 conda-forge
glib-tools 2.82.2 h4833e2c_1 conda-forge
gnuplot 5.4.10 hb1719d7_0 conda-forge
grapheme 0.6.0 pyhd8ed1ab_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
gsl 2.7 he838d99_0 conda-forge
gst-plugins-base 1.24.7 h0a52356_0 conda-forge
gstreamer 1.24.7 hf3bb09a_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
harfbuzz 10.3.0 h76408a6_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
htslib 1.21 h566b1c6_1 bioconda
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.10 pyhd8ed1ab_0 conda-forge
isa-l 2.31.1 hb9d3cd8_1 conda-forge
k8 1.2 h6618dc6_1 bioconda
kernel-headers_linux-64 3.10.0 he073ed8_18 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libasprintf 0.23.1 h8e693c7_0 conda-forge
libasprintf-devel 0.23.1 h8e693c7_0 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libcap 2.71 h39aace5_0 conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libclang-cpp19.1 19.1.7 default_hb5137d0_1 conda-forge
libclang13 19.1.7 default_h9c6a7e4_1 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.12.1 h332b0f4_0 conda-forge
libdeflate 1.23 h4ddbbb0_0 conda-forge
libdrm 2.4.124 hb9d3cd8_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libegl 1.7.0 ha4b6fd6_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.4 h5888daf_0 conda-forge
libffi 3.4.6 h2dba641_0 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-devel_linux-64 14.2.0 h9c4974d_102 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgcrypt-lib 1.11.0 hb9d3cd8_2 conda-forge
libgd 2.3.3 h6f5c62b_11 conda-forge
libgettextpo 0.23.1 h5888daf_0 conda-forge
libgettextpo-devel 0.23.1 h5888daf_0 conda-forge
libgfortran 14.2.0 h69a702a_2 conda-forge
libgfortran5 14.2.0 hf1ad2bd_2 conda-forge
libgl 1.7.0 ha4b6fd6_2 conda-forge
libglib 2.82.2 h2ff4ddf_1 conda-forge
libglvnd 1.7.0 ha4b6fd6_2 conda-forge
libglx 1.7.0 ha4b6fd6_2 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
libgpg-error 1.51 hbd13f7d_1 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libidn2 2.3.7 hd590300_0 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 31_h7ac8fdf_openblas conda-forge
libllvm19 19.1.7 ha7bfdaf_1 conda-forge
liblzma 5.6.4 hb9d3cd8_0 conda-forge
liblzma-devel 5.6.4 hb9d3cd8_0 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
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libogg 1.3.5 h4ab18f5_0 conda-forge
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libopus 1.3.1 h7f98852_1 conda-forge
libpciaccess 0.18 hd590300_0 conda-forge
libpng 1.6.47 h943b412_0 conda-forge
libpq 17.4 h27ae623_0 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsqlite 3.49.1 hee588c1_1 conda-forge
libssh2 1.11.1 hf672d98_0 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 conda-forge
libsystemd0 257.3 h3dc2cb9_0 conda-forge
libtiff 4.7.0 hd9ff511_3 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.5.0 h851e524_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.8.0 hc4a0caf_0 conda-forge
libxml2 2.13.6 h8d12d68_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
loguru 0.7.2 py38h578d9bd_1 conda-forge
lz4-c 1.10.0 h5888daf_1 conda-forge
mash 2.3 hb105d93_9 bioconda
miniasm 0.3 h577a1d6_5 bioconda
minimap2 2.28 h577a1d6_4 bioconda
mpg123 1.32.9 hc50e24c_0 conda-forge
mysql-common 9.0.1 h266115a_4 conda-forge
mysql-libs 9.0.1 he0572af_4 conda-forge
ncbi-vdb 3.2.0 h9948957_0 bioconda
ncurses 6.5 h2d0b736_3 conda-forge
nspr 4.36 h5888daf_0 conda-forge
nss 3.108 h159eef7_0 conda-forge
numpy 1.24.4 py38h59b608b_0 conda-forge
openjdk 23.0.2 h68779a4_0 conda-forge
openldap 2.6.9 he970967_0 conda-forge
openssl 3.4.1 h7b32b05_0 conda-forge
packaging 24.2 pyhd8ed1ab_2 conda-forge
pandas 2.0.3 py38h01efb38_1 conda-forge
pango 1.56.1 h861ebed_0 conda-forge
pcre2 10.44 hba22ea6_2 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge
perl-compress-raw-bzip2 2.201 pl5321hbf60520_0 conda-forge
perl-compress-raw-zlib 2.202 pl5321hadc24fc_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-filesys-df 0.92 pl5321h7b50bb2_9 bioconda
perl-io-compress 2.201 pl5321h503566f_4 bioconda
perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda
perl-json 4.10 pl5321hdfd78af_1 bioconda
perl-json-xs 4.03 pl5321h9948957_4 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h7b50bb2_4 bioconda
perl-parent 0.243 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321hb9d3cd8_1 conda-forge
perl-scalar-list-utils 1.68 pl5321hb9d3cd8_0 conda-forge
perl-storable 3.15 pl5321hb9d3cd8_0 conda-forge
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
pip 24.3.1 pyh8b19718_0 conda-forge
pixman 0.44.2 h29eaf8c_0 conda-forge
plassembler 1.6.2 pyhdfd78af_0 bioconda
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pulseaudio-client 17.0 hb77b528_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pyrodigal 3.6.3 py38h0020b31_0 bioconda
pysam 0.22.1 py38h2d19e03_2 bioconda
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.8.20 h4a871b0_2_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.2 pyhd8ed1ab_0 conda-forge
python_abi 3.8 5_cp38 conda-forge
pytz 2024.2 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py38h2019614_0 conda-forge
qt-main 5.15.15 hc3cb62f_2 conda-forge
racon 1.5.0 h077b44d_6 bioconda
raven-assembler 1.8.3 h5ca1c30_3 bioconda
readline 8.2 h8c095d6_2 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
rpsbproc 0.5.0 hd6d6fdc_2 bioconda
samtools 1.21 h96c455f_1 bioconda
setuptools 75.3.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
spades 4.1.0 haf24da9_0 bioconda
sysroot_linux-64 2.17 h0157908_18 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tzdata 2025a h78e105d_0 conda-forge
unicycler 0.5.1 py38h40d3509_2 bioconda
urllib3 2.2.3 pyhd8ed1ab_0 conda-forge
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.1 hb711507_2 conda-forge
xcb-util-image 0.4.0 hb711507_2 conda-forge
xcb-util-keysyms 0.4.1 hb711507_0 conda-forge
xcb-util-renderutil 0.3.10 hb711507_0 conda-forge
xcb-util-wm 0.4.2 hb711507_0 conda-forge
xkeyboard-config 2.43 hb9d3cd8_0 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.5 he73a12e_0 conda-forge
xorg-libx11 1.8.11 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdamage 1.1.6 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.1 hb9d3cd8_0 conda-forge
xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge
xorg-libxrandr 1.5.4 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge
xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge
xorg-libxxf86vm 1.1.6 hb9d3cd8_0 conda-forge
xz 5.6.4 hbcc6ac9_0 conda-forge
xz-gpl-tools 5.6.4 hbcc6ac9_0 conda-forge
xz-tools 5.6.4 hb9d3cd8_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstandard 0.19.0 py38h0a891b7_0 conda-forge
zstd 1.5.7 hb8e6e7a_1 conda-forge
Basic information on how to use this tool:
- executable: plassembler
- help: --help
- version: --version
- description: |
plassembler is a program that is designed for automated & fast assembly of plasmids in bacterial genomes that have been hybrid sequenced with long read & paired-end short read sequencing. It was originally designed for Oxford Nanopore Technologies long reads, but it will also work with Pacbio reads. As of v1.3.0, it also works well for long-read only assembled genomes.
Additional information:
The plsdb database that plassembler uses has been pre-downloaded at /plassembler_db using the following command:
plassembler download -d /plassembler_db
Full documentation: https://github.com/gbouras13/plassembler
plassembler run \
-l nanopore.fastq.gz \
-1 illumina_R1.fastq.gz \
-2 illumina_R2.fastq.gz \
-d /plassembler_db \
-o <output_directory> \
-t <threads> \
-c <chromosome size>