Commands done and planned

The commands that luish-extra completes, and those it is to complete, by plugin: What is supported says which are done, and completion-todo.md ticks each one that is, with the version it was checked against. A command is on this list because a lab uses it, or because it is among the most downloaded command-line tools on Bioconda: the top 2000 packages once R, Perl and Python packages are set aside, which is down to about 21,000 total downloads, plus the widely used tools further down that list and the ones that Bioconda barely carries (licensed, vendor or GitHub-only tools). Outside bio, a command may also be on it because its package is among the most downloaded on conda-forge (July to September 2026, from Anaconda’s public download statistics) and is used from the command line, not only installed as a dependency. Libraries (pysam, biopython, …), R, Perl and Bioconductor packages, and packages that only provide a library are left out.

Commands that luish’s standard completion plugin already completes (uv, pixi, micromamba, pip, conda, mamba, fd, rg, jq, zstd, sqlite3, tmux, nvim, loginctl, docker, podman, rclone, rsync, …) are not repeated here. Commands that only the bash-completion bridge covers are still listed: the plugins here are preferred, and the bridge is the fallback.

Several Bioconda packages provide commands under other names, so completion is by command name, not package name: htslib (bgzip, tabix, htsfile), blast (blastn and the rest), gatk4, spades, abyss, mmseqs2, hhsuite, ensembl-vep, primer3, subread, trim-galore, kalign2 / kalign3, t-coffee, transdecoder, rtg-tools, picard-slim, mummer4, bwameth, lumpy-sv, kmer-jellyfish, snakemake-minimal.

Every command gets its options and subcommands. Where it makes sense, arguments and option values are completed by kind: FASTA, FASTQ, BAM and other files by extension, reference names, presets, output formats, and so on.

bio: bioinformatics

Alignment files, variants and intervals

samtools, bcftools, bedtools, tabix, bgzip, htsfile, vcftools, bamtools, sambamba, samblaster, mosdepth, picard, gatk, bamutil, bam-readcount, bamhash, cramino, deeptools (bamCoverage, bamCompare, computeMatrix, plotHeatmap, plotProfile, …), bedops, vcflib, vt, snpEff, SnpSift, vep, plink, plink2, admixture, whatshap, freebayes, lofreq, varscan, octopus, bcbio-variation, delly, manta, lumpy, smoove, sniffles, cuteSV, svim, pindel, survivor, truvari, hap.py, rtg, fgbio, bwameth.py, bismark, MethylDackel, wiggletools, mummer / nucmer, alfred, gridss, varlociraptor, vardict, strelka, somaticseq, deepvariant, clair3, svtyper, svtools, duphold, samplot, annotsv, paragraph, graphtyper, vg, expansionhunter, trgt, hiphase, sawfish, gangstr, slivar, vcfanno, peddy, somalier, verifybamid2, vembrane, vcf2maf, gemini, genmod, ascat, control-freec, sequenza-utils, cnvpytor, wisecondorx, snp-sites, snp-dists, gofasta, ivar, nextalign, vadr, tn93, pyfaidx (faidx), bx-python scripts, gffutils-cli, pyfastx, crossmap

UCSC Kent tools: bedGraphToBigWig, bedToBigBed, bigWigToWig, bigWigToBedGraph, bigWigInfo, bigBedToBed, bigBedInfo, wigToBigWig, faToTwoBit, twoBitToFa, twoBitInfo, faSize, faFrag, faSomeRecords, liftOver, gtfToGenePred, genePredToBed, genePredToGtf, gff3ToGenePred, blat, pslCDnaFilter, pslSort, bedSort, bedClip, bedIntersect, fetchChromSizes, chainNet, axtChain, and the rest of the ucsc-* packages

Mapping and quantification

bwa, bwa-mem2, bowtie, bowtie2, bowtie2-build, minimap2, hisat2, hisat2-build, STAR, gmap, lastal, lastdb, last-train and the other LAST tools, kallisto, bustools, salmon, stringtie, htseq-count, featureCounts, rsem-calculate-expression, cufflinks, regtools, tophat, chromap, strobealign, ngmlr, segemehl, graphmap, snap-aligner, novoalign, yara_mapper, mash, sourmash, fastANI, skani, sylph, STAR-Fusion, arriba, fusioncatcher, qualimap, umi_tools, preseq, rmats, suppa, portcullis, mikado, rnaquast, trinotate, corset, scallop, psiclass, flair, isoquant, oarfish, alevin-fry, simpleaf, kb, velocyto, kma, rseqc scripts (bam_stat.py, …)

Read QC, trimming and sequence utilities

fastp, fastqc, falco, multiqc, cutadapt, trimmomatic, trim_galore, AdapterRemoval, atropos, flexbar, fastx_* (fastx_toolkit), bbduk.sh and the other BBMap tools, seqkit, seqtk, csvtk, seqfu, seqmagick, bioawk, filtlong, chopper, nanoq, rasusa, NanoPlot, NanoFilt, NanoStat, porechop, fastq_screen (fastq-screen), fastq-dl, kmc, jellyfish, meryl, khmer, pear, flash, sickle, lighter, pigz, pixz, taxonkit, sga, kat, genomescope2, smudgeplot, nanocomp, pycoqc, toulligqc, pomoxis

Assembly, annotation and polishing

spades.py, metaspades.py, megahit, abyss-pe, velveth, velvetg, unicycler, shovill, skesa, flye, canu, hifiasm, miniasm, wtdbg2, raven, verkko, racon, medaka, pilon, polypolish, quast, busco, merqury, prodigal, prokka, bakta, pharokka, barrnap, tRNAscan-SE, aragorn, augustus, braker.pl, TransDecoder.LongOrfs, gffread, gffcompare, agat_*, RepeatMasker, RepeatModeler, trf, maker, Trinity, funannotate, liftoff, ragtag.py, masurca, soapdenovo2, minia, idba, velvet, gfastats, compleasm, edta, earlgrey, ltr_retriever, tesorter, evidencemodeler, pasa, gemoma, miniprot, spaln, glimmerhmm, snap, codingquarry, shasta, nextdenovo, nextpolish, purge_dups, yahs, trycycler, dragonflye, plassembler, hybracter, metamdbg, jcvi

Long reads

f5c, slow5tools, pod5, nanopolish, megalodon, modkit, pbmm2, ccs, lima, isoseq3, pbsv, longshot, winnowmap, savana, dorado, guppy_basecaller, guppy_barcoder, smrtlink tools

Comparative genomics, pangenomes and population genetics

orthofinder, proteinortho, sonicparanoid, pantools, anchorwave, wgd, cactus, minigraph, wfmash, pggb, odgi, seqwish, mashmap, syri, plotsr, stacks (ustacks, cstacks, …), ipyrad, ddocent, angsd, admixtools, smartpca, treemix, gcta, regenie, shapeit4, beagle, king, selscan, bolt, impute2, glimpse, rfmix

Hi-C and epigenomics

hicexplorer (hicFindTADs, …), cooler, cooltools, pairtools, pairix, chromosight, hictk, epic2, genrich, chromhmm, idr, phantompeakqualtools, ataqv, dnmtools, biscuit, methylpy, moabs, bsmap, methylartist

Alignment and phylogenetics

mafft, muscle, clustalw, clustalo, t_coffee, kalign, probcons, trimal, clipkit, FastTree, iqtree / iqtree2, raxml-ng, raxmlHPC, phyml, mrbayes, beast, hyphy, paml (codeml, …), gappa, epa-ng, pplacer, treetime, gotree, goalign, ete3, quicktree, rapidnj, sepp, phylip, prank, pasta, poa, famsa, pal2nal, gblocks, macse, generax, modeltest-ng, veryfasttree, aster, figtree, tracer, beast2, revbayes, bali-phy, fastme, newick_utils, phykit, sumtrees.py, emboss (needle, water, …)

Metagenomics and microbial genomics

kraken2 (kraken2-build, kraken2-inspect, k2), bracken (bracken-build, combine_bracken_outputs.py), krakenuniq (krakenuniq-build, krakenuniq-report, krakenuniq-download), centrifuge (centrifuge-build, centrifuge-inspect, centrifuge-kreport), kaiju (kaiju-multi, kaiju2table, kaiju2krona, kaiju-addTaxonNames, kaiju-mergeOutputs, kaiju-makedb, kaiju-mkbwt, kaiju-mkfmi), metaphlan (merge_metaphlan_tables.py, strainphlan, sample2markers.py, extract_markers.py), humann (humann_databases, humann_config, humann_join_tables, humann_renorm_table, humann_regroup_table, humann_split_stratified_table, humann_rename_table, humann_split_table, humann_reduce_table, humann_unpack_pathways, humann_barplot), motus, checkm, checkm2, checkv, gunc, singlem, gtdbtk, metabat2 (jgi_summarize_bam_contig_depths), concoct (concoct_coverage_table.py, cut_up_fasta.py, merge_cutup_clustering.py, extract_fasta_bins.py), run_MaxBin.pl (MaxBin), DAS_Tool (Fasta_to_Contig2Bin.sh), dRep, coverm, vamb, genomad, emapper.py (download_eggnog_data.py, create_dbs.py, hmm_mapper.py), mothur, qiime, picrust2, humann, krona, abricate, amrfinder (amrfinder_update), rgi, mlst, snippy, roary, panaroo, ppanggolin, gubbins, prokka, srst2, sistr, ectyper, seqsero2, kleborate, ariba, staramr, mykrobe, tb-profiler, bactopia, anvi-* (anvio), phispy, antismash, metawrap, phyloflash, graftm, dram, vibrant, virsorter, vcontact2, iphop, phabox, instrain, binsanity, comebin, metacoag, binette, kmcp, ganon, metacache, krakentools, kraken-biom, taxpasta, metaeuk, insilicoseq, unifrac, deblur, gneiss, emperor, lefse, maaslin2, thapbi-pict, harpy, resfinder, plasmidfinder, mob_suite, hamronization, defense-finder, macsyfinder, integron_finder, islandpath, bigscape, deepbgc, gecco, kaptive, pyani, parsnp, mashtree, poppunk, pyseer, scoary, pirate, chewbbaca, ska2, mentalist, ntm-profiler, nullarbor, dnaapler, pyrodigal, phanotate, minced, platon, plasmidid

Data access

esearch, efetch, elink, esummary, xtract and the other entrez-direct tools, prefetch, fasterq-dump, fastq-dump, vdb-validate and the other sra-tools, datasets, dataformat, ncbi-genome-download, genome_updater, gdc-client, aria2c, dx (dxpy), ascp (aspera-cli), ena-webin-cli, ena-upload-cli, pyega3, kingfisher, pysradb, geofetch, ffq, parallel-fastq-dump, refgenie, genomepy, bioconvert, pygenometracks, igv-reports, igvtools, gw, jbrowse2, asciigenome, goatools, gseapy, biom

Proteomics and mass spectrometry

comet, peptide-shaker, searchgui, openms (*Tool binaries), maxquant, msgf_plus, percolator, ThermoRawFileParser, msconvert (proteowizard), crux, sage, flashlfq, msstitch, pyprophet, easypqp, ms2rescore, sirius, metfrag, mzmine

Structure, immunology and CRISPR

TMalign, USalign, openstructure, anarci, abnumber, igblast, changeo scripts, presto scripts, igdiscover, trust4, optitype, hla-la, arcas-hla, seq2hla, mhcflurry, crisprme, crispresso2, crispritz, coot, relion, smina, rxdock, obabel (openbabel), mgltools, colabfold_batch, run_alphafold.py, boltz, chai

Other

ngless (and .ngl scripts), SemiBin2 / SemiBin, macrel, argnorm, gmsc-mapper, nextclade, pangolin, augur, auspice, usher, freyja, artic, primer3_core, RNAfold and the other ViennaRNA tools, meme, fimo and the other MEME suite tools, homer, macs2 / macs3, sicer, mageck, cnvkit.py, circos, igv, jbrowse, bandage, weblogo, cellranger-style single-cell tools such as cellsnp-lite, and, from outside Bioconda, cellranger, cellranger-atac, spaceranger, bcl2fastq, bcl-convert, dragen, pbrun (Parabricks), table_annovar.pl and the other ANNOVAR scripts, gmes_petap.pl (GeneMark), signalp6, tmhmm, netMHCpan, ldsc.py, PRSice, saige, shapeit5, eagle, stitch, pixy, flashpca, cellbender, vireo, souporcell

science: general scientific computing

  • Workflows: jug (subcommands, and jugfiles *.py as arguments), snakemake (rules from the Snakefile as targets), nextflow, nf-core, nf-test, cwltool, cromwell, toil, planemo, dagster

  • Writing: quarto, latexmk, pdflatex, xelatex, bibtex, biber, pandoc, tectonic

  • Interactive Python and R: ipython, jupyter, Rscript, R, marimo, jupytext

  • Plotting and numerics: gnuplot, glpk (glpsol), datamash, tsv-utils, Graphviz (dot, neato, fdp, sfdp, circo, twopi: output formats and layouts from the installed dot)

  • Tabular data: mlr (Miller), xsv / qsv, duckdb

  • Parallel and distributed computing: mpirun / mpiexec (Open MPI, MPICH), dask, ray, spark-submit, pyspark

  • Geospatial: GDAL (gdal, the command of GDAL 3.11 and later, and gdalinfo, gdal_translate, gdalwarp, gdalbuildvrt, ogr2ogr, ogrinfo), PROJ (proj, cs2cs, projinfo)

  • Data formats: netCDF (ncdump, nccopy, ncgen), HDF5 (h5dump, h5ls, h5diff, h5repack), ecCodes (grib_ls, grib_dump, grib_copy)

  • Chemistry and molecular modelling: gromacs (gmx), autodock-vina, AmberTools (tleap, cpptraj, pmemd), namd, lmp

  • General command-line utilities that Bioconda ships: parallel, aria2c, pigz, singularity / apptainer, aws (awscli)

gui: desktop programs

  • Browsers and mail: firefox (profiles for -P), chromium, google-chrome, thunderbird

  • Documents: libreoffice / soffice (--convert-to formats), evince, okular, zathura, xdg-open

  • Editors: code (installed extensions for --uninstall-extension), meld, gedit, kate

  • Media and graphics: vlc (and cvlc), mpv, gimp, inkscape, krita, blender, obs, audacity, eog

  • Bioinformatics viewers: cytoscape, jalview, artemis (art, act, bamview, dnaplotter), tablet, bandage_ng (BandageNG), proksee, pymol, chimerax, vmd

  • Desktop tools: xrandr, gsettings, dconf, notify-send, wmctrl, xdotool, swaymsg, hyprctl

dev: development and deployment

  • Environments and packaging: poetry (the groups, extras, dependencies and sources of pyproject.toml, the packages of poetry.lock), twine (the repositories of ~/.pypirc), pre-commit and prek (the hooks of .pre-commit-config.yaml), virtualenv, tox, pipx

  • conda-forge packaging: conda-build (also conda build, conda render and conda debug; recipe directories and variant files), rattler-build, conda-smithy, grayskull, conda-pack, conda-lock

  • Python tooling: pytest (test files and the tests in them, FILE::CLASS::TEST; markers; the options of pytest-xdist and pytest-cov), ruff (rule codes and linter prefixes), mypy (error codes), coverage, isort, pylint (message IDs), flake8, autopep8, yapf, pyright, ty, cython / cythonize, nbstripout, Sphinx (sphinx-build, with builders for -b; sphinx-apidoc, sphinx-quickstart)

  • Compilers and runtimes: gfortran, nvcc, rustc, node, OpenJDK (java, javac, jar, keytool), ruby, gem

  • Build tools: just (the recipes of the justfile), pkg-config (packages from pkg-config --list-all), ccache, sccache, bazel, scons, doxygen, protoc

  • C and C++ tools: clang-format, clang-tidy (checks from clang-tidy --list-checks), clangd, cppcheck

  • Linters and formatters: shellcheck (check codes; optional checks from --list-optional), prettier, typos, taplo, zizmor, lefthook

  • Task runners: inv / invoke, fab (Fabric), through their own --complete

  • Web services: gunicorn, fastapi, django-admin (through Django’s own completion), caddy, mitmproxy, mitmdump

  • Databases: PostgreSQL (psql, pg_dump, pg_restore, pg_dumpall, pg_ctl, initdb, createdb, dropdb; databases from psql -l)

  • Machine learning: hf (huggingface_hub), accelerate

  • Infrastructure: terraform, buf, yq, databricks

  • Command-line utilities: fzf, bat (batcat on Debian; its languages and themes)

  • Coding agents: claude (read from its help; the agents of .claude/agents for --agent), codex (read from its help; the profiles of $CODEX_HOME for --profile), opencode

  • Version control: svn, git lfs (std’s git completer hands git lfs over to the completer of git-lfs)

  • Web deployment: netlify

  • Android: adb

system: system administration

  • Backups: borg

  • Filesystems: fusermount / fusermount3 (the FUSE mount points, for -u)

  • Archives: 7zz / 7z (7-Zip, p7zip)

  • Version control: git-annex (completed by git-annex itself; also git annex, which std’s git completer hands over)

media: audio, video and images

  • Audio and video: ffmpeg (the options of an input or an output, with the private options of the codecs and the format chosen for it; codecs, formats, filters and pixel formats from the installed ffmpeg; filtergraphs; the streams of the inputs, for -map)

  • Images: magick, convert (ImageMagick’s older name), gm (GraphicsMagick), vips, tesseract (languages from tesseract --list-langs)

  • PDF and PostScript: Poppler (pdftotext, pdfinfo, pdftoppm, pdfimages, pdfunite, pdfseparate), gs (Ghostscript; devices from gs -h), qpdf

  • Downloads: yt-dlp

hpc: HPC clusters

  • Slurm: sbatch, salloc, srun, squeue, scancel, sinfo, sacct (partitions, accounts, QOS, nodes, features, GRES, licenses, reservations and the user’s jobs from the cluster; the command that srun and salloc run is completed by its own completer), scontrol, sacctmgr

  • Other schedulers: qsub (PBS, SGE), bsub (LSF)

  • Environment modules: module

  • Data transfer: s5cmd, globus

Possible later plugins

  • cloud: gcloud, az (and aws, which science completes already)