Main tool: autocycler
Code repository: https://github.com/rrwick/Autocycler/
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
alsa-lib 1.2.11 hd590300_1 conda-forge
any2fasta 0.4.2 hdfd78af_3 bioconda
attr 2.5.1 h166bdaf_1 conda-forge
bwa 0.7.18 he4a0461_1 bioconda
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.4 hb9d3cd8_0 conda-forge
ca-certificates 2025.1.31 hbcca054_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
canu 2.2 ha47f30e_0 bioconda
dbus 1.13.6 h5008d03_3 conda-forge
expat 2.6.4 h5888daf_0 conda-forge
flye 2.9.5 py312ha1f7cf2_1 bioconda
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
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 2.80.2 hf974151_0 conda-forge
glib-tools 2.80.2 hb6ce0ca_0 conda-forge
gnuplot 5.4.10 hb1719d7_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
gst-plugins-base 1.24.4 h9ad1361_0 conda-forge
gstreamer 1.24.4 haf2f30d_0 conda-forge
harfbuzz 8.5.0 hfac3d4d_0 conda-forge
htslib 1.21 h5efdd21_0 bioconda
icu 73.2 h59595ed_0 conda-forge
k8 1.2 h6618dc6_3 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 2.16 hb7c19ff_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
libcap 2.71 h39aace5_0 conda-forge
libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge
libclang13 18.1.7 default_h087397f_0 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.8.0 hca28451_1 conda-forge
libdeflate 1.20 hd590300_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 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-ng 14.2.0 h69a702a_2 conda-forge
libgcrypt-lib 1.11.0 hb9d3cd8_2 conda-forge
libgd 2.3.3 h119a65a_9 conda-forge
libgettextpo 0.23.1 h5888daf_0 conda-forge
libgettextpo-devel 0.23.1 h5888daf_0 conda-forge
libglib 2.80.2 hf974151_0 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
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libllvm18 18.1.7 hb77312f_0 conda-forge
liblzma 5.6.4 hb9d3cd8_0 conda-forge
liblzma-devel 5.6.4 hb9d3cd8_0 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.5 h4ab18f5_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libpq 16.8 h87c4ccc_0 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_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 4.6.0 h1dd3fc0_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp 1.4.0 h2c329e2_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.7.0 h662e7e4_0 conda-forge
libxml2 2.12.7 hc051c1a_1 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
lja 0.2 h5b5514e_2 bioconda
lz4-c 1.10.0 h5888daf_1 conda-forge
metamdbg 1.0 hdcf5f25_1 bioconda
miniasm 0.3 he4a0461_3 bioconda
minimap2 2.28 he4a0461_3 bioconda
minipolish 0.1.3 pyhdfd78af_0 bioconda
mpg123 1.32.9 hc50e24c_0 conda-forge
mysql-common 8.3.0 hf1915f5_4 conda-forge
mysql-libs 8.3.0 hca2cd23_4 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
necat 0.0.1_update20200803 h43eeafb_5 bioconda
nextdenovo 2.5.2 py312ha5a3fb2_5 bioconda
nextpolish 1.4.1 py312ha5a3fb2_3 bioconda
nspr 4.36 h5888daf_0 conda-forge
nss 3.100 hca3bf56_0 conda-forge
openjdk 22.0.1 hb622114_0 conda-forge
openssl 3.4.1 h7b32b05_0 conda-forge
pango 1.54.0 h84a9a3c_0 conda-forge
paralleltask 0.1.1 pyhd8ed1ab_0 conda-forge
pcre2 10.43 hcad00b1_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
perl-env 1.04 pl5321hd8ed1ab_0 conda-forge
perl-filesys-df 0.92 pl5321h7b50bb2_9 bioconda
pip 25.0.1 pyh8b19718_0 conda-forge
pixman 0.44.2 h29eaf8c_0 conda-forge
psutil 6.1.1 py312h66e93f0_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
pulseaudio-client 17.0 hb77b528_0 conda-forge
python 3.12.3 hab00c5b_0_cpython conda-forge
python-edlib 1.3.9.post1 py312hf731ba3_1 bioconda
python_abi 3.12 5_cp312 conda-forge
qt-main 5.15.8 hc9dc06e_21 conda-forge
racon 1.5.0 hdcf5f25_5 bioconda
raven-assembler 1.8.3 h43eeafb_1 bioconda
readline 8.2 h8c095d6_2 conda-forge
samtools 1.21 h50ea8bc_0 bioconda
seqtk 1.4 he4a0461_2 bioconda
setuptools 75.8.0 pyhff2d567_0 conda-forge
sysroot_linux-64 2.17 h0157908_18 conda-forge
time 1.8 hd590300_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tzdata 2025a h78e105d_0 conda-forge
wheel 0.45.1 pyhd8ed1ab_1 conda-forge
wtdbg 2.5 h43eeafb_4 bioconda
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.42 h4ab18f5_0 conda-forge
xorg-fixesproto 5.0 hb9d3cd8_1003 conda-forge
xorg-inputproto 2.3.2 hb9d3cd8_1003 conda-forge
xorg-kbproto 1.0.7 hb9d3cd8_1003 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.5 he73a12e_0 conda-forge
xorg-libx11 1.8.9 h8ee46fc_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h4bc722e_1 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-libxt 1.3.0 hd590300_1 conda-forge
xorg-libxtst 1.2.5 h4bc722e_0 conda-forge
xorg-recordproto 1.14.2 hb9d3cd8_1003 conda-forge
xorg-renderproto 0.11.1 hb9d3cd8_1003 conda-forge
xorg-xextproto 7.3.0 hb9d3cd8_1004 conda-forge
xorg-xf86vidmodeproto 2.3.1 hb9d3cd8_1005 conda-forge
xorg-xproto 7.0.31 hb9d3cd8_1008 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
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: autocycler
- help: --help
- version: --version
- description: |
Autocycler is a tool for generating consensus long-read assemblies for bacterial genomes.
Additional information:
This image contains all additional tools listed in the environmental.yml file.
Full documentation: https://github.com/rrwick/Autocycler/wiki
reads=ont.fastq.gz # your read set goes here
threads=16 # set as appropriate for your system
genome_size=$(genome_size_raven.sh "$reads" "$threads") # can set this manually if you know the value
# Step 1: subsample the long-read set into multiple files
autocycler subsample --reads "$reads" --out_dir subsampled_reads --genome_size "$genome_size"
# Step 2: assemble each subsampled file
mkdir assemblies
for assembler in canu flye miniasm necat nextdenovo raven; do
for i in 01 02 03 04; do
"$assembler".sh subsampled_reads/sample_"$i".fastq assemblies/"$assembler"_"$i" "$threads" "$genome_size"
done
done
# Optional step: remove the subsampled reads to save space
rm subsampled_reads/*.fastq
# Step 3: compress the input assemblies into a unitig graph
autocycler compress -i assemblies -a autocycler_out
# Step 4: cluster the input contigs into putative genomic sequences
autocycler cluster -a autocycler_out
# Steps 5 and 6: trim and resolve each QC-pass cluster
for c in autocycler_out/clustering/qc_pass/cluster_*; do
autocycler trim -c "$c"
autocycler resolve -c "$c"
done
# Step 7: combine resolved clusters into a final assembly
autocycler combine -a autocycler_out -i autocycler_out/clustering/qc_pass/cluster_*/5_final.gfa