count	counting
filtering	preprocessing
fastqc	preprocessing
fastp	preprocessing
cutadapt	preprocessing
atropos	preprocessing
hifiadapterfilt	preprocessing
kneaddata	preprocessing
mapdamage2	preprocessing
simka	distance measure
flash	paired-read merging
ngmerge	paired-read merging
pear	paired-read merging
bbmerge	paired-read merging
bowtie2	alignment
minimap2	alignment
salmon	alignment
kallisto	alignment
mapping	alignment
mapping_filtering	alignment
mapping_fastp	alignment
mapping_cutadapt	alignment
mapping_atropos	alignment
mapping_kneaddata	alignment
mapping_flash	alignment
mapping_ngmerge	alignment
mapping_pear	alignment
mapping_bbmerge	alignment
pysam	alignment
pysam_megahit	alignment
pysam_spades	alignment
pysam_flye	alignment
pysam_canu	alignment
pysam_unicycler	alignment
pysam_miniasm	alignment
pysam_spades_plasmid	alignment
pysam_spades_metaviral	alignment
pysam_spades_bio	alignment
pysam_prodigal	alignment
mmseqs2	annotation (protein prediction)
prodigal	annotation (protein prediction)
macsyfinder	annotation (macromolecular systems, pathways)
integronfinder	annotation (integrons)
search_diamond	annotation (proteins)
search_hmmer	annotation (proteins)
prokka	annotation (genome)
barrnap	annotation (rRNA)
ccfind	annotation (circularity)
circlator	annotation (circularity)
antismash	annotation (antibiotics and secondary metabolite)
tiara	annotation (eukaryotic sequences)
metaclade2	annotation (protein domains)
deeptmhmm	annotation (transmembrane proteins)
itasser	annotation (proteins)
itassermtd	annotation (proteins)
graspx	annotation (genes)
rundbcan	annotation (CAZy)
ioncom	annotation (cations)
diting	annotation (pathways)
keggcharter	annotation (pathways)
metacompare	annotation (ARGs)
deeparg	annotation (ARGs)
deeparg_predict	annotation (ARGs)
deeparg_short	annotation (ARGs)
metamarc	annotation (ARGs)
karga	annotation (ARGs)
kargva	annotation (ARGs)
abritamr	annotation (ARGs)
abricate	annotation (ARGs)
amrplusplus2	annotation (ARGs)
amrfinderplus	annotation (ARGs)
staramr	annotation (ARGs)
argsoap	annotation (ARGs)
hamronization	annotation (ARGs)
size	annotation (length)
pooling	coassembly setup
quast	assembling (quality check)
spades	assembling
spades_metaviral	assembling (viruses)
spades_plasmid	assembling (plasmids)
spades_bio	assembling (biosynthetic gene clusters)
megahit	assembling
plass	assembling (protein-level)
flye	assembling
canu	assembling
unicycler	assembling
miniasm	assembling
necat	assembling
metamic	assembling
metawrap_quantify	binning
metawrap_classify	binning
metawrap_annotate	binning
metawrap_blobology	binning
metawrap_reassemble	binning
metawrap_refine	binning
metawrap_binning	binning
metawrap	binning
yamb	binning
mycc	binning
binspreader	binning
groopm	binning
vamb	binning
mycc	binning
drep	MAG (dereplication)
skani	MAG (comparison)
gtdbtk	MAG (quality check)
checkm_tree	MAG (quality check)
checkm_treeqa	MAG (quality check)
checkm_lineageset	MAG (quality check)
checkm_analyze	MAG (quality check)
checkm_coverage	MAG (quality check)
checkm_qa	MAG (quality check)
checkm_unbinned	MAG (quality check)
checkm_tetra	MAG (quality check)
checkm	MAG (quality check)
checkm2	MAG (quality check)
busco	MAG (quality check)
metamarker	profiling
midas	profiling
midas2_snps	profiling
midas2_genes	profiling
midas2_species	profiling
midas2	profiling
metaphlan	profiling
humann	profiling
shogun	profiling
kaiju	profiling
woltka	profiling
kraken2	profiling
bracken	profiling
metaxa2	profiling
motus	profiling
ngless	profiling
phyloflash	profiling
closedref	profiling
squeezemeta	pipeline
anvio	pipeline
trf	repeats
kmerssr	repeats
divissr	repeats
eggnogmapper	annotation
plasmidfinder	annotation (plasmid)
plasforest	annotation (plasmid)
plasflow	annotation (plasmid)
rfplasmid	annotation (plasmid)
mobsuite	annotation (mobilome)
genomad	annotation (mobilome)
strainphlan	strain-level analysis
lorikeet_call	strain-level analysis
lorikeet_consensus	strain-level analysis
lorikeet_genotype	strain-level analysis
lorikeet	strain-level analysis
instrain	strain-level analysis
strainpro	strain-level analysis
panphlan	strain-level analysis
strainsifter	strain-level analysis
viralverify	annotation (virus)
virstrain	annotation (virus)
threecac	annotation (virus)
coconet	annotation (virus)
deepvirfinder	annotation (virus)
wish	annotation (virus)
graphlan	visualization
