Main tool: qualimap
Code repository: https://bitbucket.org/kokonech/qualimap
Basic information on how to use this tool:
- executable:
qualimap - help:
--help - version:
--help - description: the quality control of alignment sequencing data with GUI or CLI
Additional information:
Supported types of experiments:
- Whole-genome sequencing
- Whole-exome sequencing
- RNA-seq (speical mode available)
- ChIP-seq
Full documentation: http://qualimap.conesalab.org/doc_html/index.html
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
_r-mutex 1.0.1 anacondar_1 conda-forge
alsa-lib 1.2.14 hb9d3cd8_0 conda-forge
argcomplete 3.6.2 pyhd8ed1ab_0 conda-forge
binutils_impl_linux-64 2.43 h4bf12b8_4 conda-forge
bioconductor-biobase 2.66.0 r44h3df3fcb_0 bioconda
bioconductor-biocgenerics 0.52.0 r44hdfd78af_3 bioconda
bioconductor-biocio 1.16.0 r44hdfd78af_0 bioconda
bioconductor-biocparallel 1.40.0 r44he5774e6_1 bioconda
bioconductor-biostrings 2.74.0 r44h3df3fcb_1 bioconda
bioconductor-bsgenome 1.74.0 r44hdfd78af_0 bioconda
bioconductor-data-packages 20250401 hdfd78af_0 bioconda
bioconductor-delayedarray 0.32.0 r44h3df3fcb_1 bioconda
bioconductor-dnacopy 1.80.0 r44h4d5c4aa_1 bioconda
bioconductor-edger 4.4.0 r44h3df3fcb_0 bioconda
bioconductor-genomeinfodb 1.42.0 r44hdfd78af_2 bioconda
bioconductor-genomeinfodbdata 1.2.13 r44hdfd78af_0 bioconda
bioconductor-genomicalignments 1.42.0 r44h3df3fcb_1 bioconda
bioconductor-genomicranges 1.58.0 r44h3df3fcb_2 bioconda
bioconductor-iranges 2.40.0 r44h3df3fcb_2 bioconda
bioconductor-limma 3.62.1 r44h15a9599_1 bioconda
bioconductor-matrixgenerics 1.18.0 r44hdfd78af_0 bioconda
bioconductor-noiseq 2.50.0 r44hdfd78af_0 bioconda
bioconductor-repitools 1.52.0 r44he5774e6_0 bioconda
bioconductor-rhtslib 3.2.0 r44h15a9599_2 bioconda
bioconductor-rsamtools 2.22.0 r44h77050f0_1 bioconda
bioconductor-rtracklayer 1.66.0 r44h15a9599_1 bioconda
bioconductor-s4arrays 1.6.0 r44h3df3fcb_1 bioconda
bioconductor-s4vectors 0.44.0 r44h3df3fcb_2 bioconda
bioconductor-sparsearray 1.6.0 r44h3df3fcb_1 bioconda
bioconductor-summarizedexperiment 1.36.0 r44hdfd78af_0 bioconda
bioconductor-ucsc.utils 1.2.0 r44h9ee0642_1 bioconda
bioconductor-xvector 0.46.0 r44h15a9599_2 bioconda
bioconductor-zlibbioc 1.52.0 r44h3df3fcb_2 bioconda
bwidget 1.10.1 ha770c72_0 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.4.26 hbd8a1cb_0 conda-forge
cairo 1.18.4 h3394656_0 conda-forge
curl 8.13.0 h332b0f4_0 conda-forge
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 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.13.3 ha770c72_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gcc_impl_linux-64 14.2.0 hdb7739f_2 conda-forge
gfortran_impl_linux-64 14.2.0 h0ee6e4a_2 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
gsl 2.7 he838d99_0 conda-forge
gxx_impl_linux-64 14.2.0 h2ead766_2 conda-forge
harfbuzz 11.1.0 h3beb420_0 conda-forge
icu 75.1 he02047a_0 conda-forge
jq 1.7.1 hd590300_0 conda-forge
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
lcms2 2.17 h717163a_0 conda-forge
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
lerc 4.0.0 h0aef613_1 conda-forge
libblas 3.9.0 31_h59b9bed_openblas conda-forge
libcblas 3.9.0 31_he106b2a_openblas conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libcurl 8.13.0 h332b0f4_0 conda-forge
libdeflate 1.23 h86f0d12_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.0 h5888daf_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libfreetype 2.13.3 ha770c72_1 conda-forge
libfreetype6 2.13.3 h48d6fc4_1 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
libgfortran 14.2.0 h69a702a_2 conda-forge
libgfortran-ng 14.2.0 h69a702a_2 conda-forge
libgfortran5 14.2.0 hf1ad2bd_2 conda-forge
libglib 2.84.1 h2ff4ddf_0 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libjpeg-turbo 3.1.0 hb9d3cd8_0 conda-forge
liblapack 3.9.0 31_h7ac8fdf_openblas conda-forge
liblzma 5.8.1 hb9d3cd8_0 conda-forge
libmpdec 4.0.0 h4bc722e_0 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libopenblas 0.3.29 pthreads_h94d23a6_0 conda-forge
libpng 1.6.47 h943b412_0 conda-forge
libsanitizer 14.2.0 hed042b8_2 conda-forge
libsqlite 3.49.1 hee588c1_2 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 14.2.0 h8f9b012_2 conda-forge
libstdcxx-devel_linux-64 14.2.0 h9c4974d_102 conda-forge
libstdcxx-ng 14.2.0 h4852527_2 conda-forge
libtiff 4.7.0 hd9ff511_4 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.5.0 h851e524_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxml2 2.13.7 h4bc477f_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
make 4.4.1 hb9d3cd8_2 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
oniguruma 6.9.10 hb9d3cd8_0 conda-forge
openjdk 23.0.2 h53dfc1b_2 conda-forge
openssl 3.5.0 h7b32b05_0 conda-forge
pango 1.56.3 h9ac818e_1 conda-forge
pcre2 10.44 hc749103_2 conda-forge
pip 25.1 pyh145f28c_0 conda-forge
pixman 0.46.0 h29eaf8c_0 conda-forge
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
python 3.13.3 hf636f53_101_cp313 conda-forge
python_abi 3.13 7_cp313 conda-forge
pyyaml 6.0.2 py313h8060acc_2 conda-forge
qualimap 2.3 hdfd78af_0 bioconda
r-abind 1.4_5 r44hc72bb7e_1006 conda-forge
r-askpass 1.2.1 r44h2b5f3a1_0 conda-forge
r-base 4.4.3 h9c32bc2_0 conda-forge
r-bh 1.87.0_1 r44hc72bb7e_0 conda-forge
r-bitops 1.0_9 r44h2b5f3a1_0 conda-forge
r-catools 1.18.3 r44h93ab643_0 conda-forge
r-cluster 2.1.8.1 r44hb67ce94_0 conda-forge
r-codetools 0.2_20 r44hc72bb7e_1 conda-forge
r-cpp11 0.5.2 r44h785f33e_1 conda-forge
r-crayon 1.5.3 r44hc72bb7e_1 conda-forge
r-curl 6.2.2 r44h2700575_0 conda-forge
r-formatr 1.14 r44hc72bb7e_2 conda-forge
r-futile.logger 1.4.3 r44hc72bb7e_1006 conda-forge
r-futile.options 1.0.1 r44hc72bb7e_1005 conda-forge
r-getopt 1.20.4 r44ha770c72_1 conda-forge
r-gplots 3.2.0 r44hc72bb7e_0 conda-forge
r-gsmoothr 0.1.7 r44hdb488b9_1007 conda-forge
r-gtools 3.9.5 r44hb1dbf0f_1 conda-forge
r-httr 1.4.7 r44hc72bb7e_1 conda-forge
r-jsonlite 2.0.0 r44h2b5f3a1_0 conda-forge
r-kernsmooth 2.23_26 r44h8461fee_0 conda-forge
r-lambda.r 1.2.4 r44hc72bb7e_4 conda-forge
r-lattice 0.22_7 r44h2b5f3a1_0 conda-forge
r-locfit 1.5_9.12 r44h2b5f3a1_0 conda-forge
r-mass 7.3_64 r44h2b5f3a1_0 conda-forge
r-matrix 1.7_3 r44h2ae2be5_0 conda-forge
r-matrixstats 1.5.0 r44h2b5f3a1_0 conda-forge
r-mime 0.13 r44h2b5f3a1_0 conda-forge
r-openssl 2.3.2 r44he8289e2_0 conda-forge
r-optparse 1.7.5 r44hc72bb7e_1 conda-forge
r-r6 2.6.1 r44hc72bb7e_0 conda-forge
r-rcurl 1.98_1.16 r44he8228da_1 conda-forge
r-restfulr 0.0.15 r44h5ef9028_6 bioconda
r-rjson 0.2.23 r44h93ab643_0 conda-forge
r-rsolnp 1.16 r44ha770c72_1006 conda-forge
r-snow 0.4_4 r44hc72bb7e_3 conda-forge
r-statmod 1.5.0 r44ha36c22a_2 conda-forge
r-sys 3.4.3 r44h2b5f3a1_0 conda-forge
r-truncnorm 1.0_9 r44h2b5f3a1_4 conda-forge
r-xml 3.99_0.17 r44h5bae778_2 conda-forge
r-yaml 2.3.10 r44hdb488b9_0 conda-forge
readline 8.2 h8c095d6_2 conda-forge
sed 4.8 he412f7d_0 conda-forge
setuptools 79.0.1 pyhff2d567_0 conda-forge
sysroot_linux-64 2.17 h0157908_18 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tktable 2.10 h8bc8fbc_6 conda-forge
toml 0.10.2 pyhd8ed1ab_1 conda-forge
tomlkit 0.13.2 pyha770c72_1 conda-forge
tzdata 2025b h78e105d_0 conda-forge
xmltodict 0.14.2 pyhd8ed1ab_1 conda-forge
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 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 6.0.1 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
yaml 0.2.5 h7f98852_2 conda-forge
yq 3.4.3 pyhd8ed1ab_1 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Using GUI
docker run -v $(pwd):/data -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=$DISPLAY staphb/qualimap:2.3 qualimap
Using CLI
# HTML report
qualimap bamqc -bam file.bam -outdir qualimap_results
# PDF report
qualimap bamqc -bam file.bam -outfile result.pdf
# RNAseq
qualimap rnaseq -bam kidney.bam -gtf human.64.gtf -outdir rnaseq_qc_results
# CountsQC
qualimap counts -d GlcN_countsqc_input.txt -c -s mouse -outdir glcn_mice_counts
# Clustering
qualimap clustering -sample clustering/hmeDIP.bam -control clustering/input.bam -regions annotations/transcripts.human.64.bed -outdir clustering_result
# Compute counts
qualimap comp-counts -bam kidney.bam -gtf ../annotations/human.64.gtf -out kidney.counts