Name	Short Description	Language
AddStrain	Add new strain	Python
AminoAcidComposition	Amino acid composition of a protein sequence (Generated by PluGen)	C++
BAMContig	Split BAM file into contigs	C++
BAMSort	Sort a BAM file	C++
BEDContig	Split BED file into contigs	C++
BedWindow	Sliding window for BED file	C++
BigWigAverageOverBed	Average of Bigwig over BED file	C++
BigCat	Multi-concatenator	C++
BIOM2CSV	Convert BIOM file to CSVA	Python
BLASTJoin	Join outputs from BLAST	C++
ClosestBED	Search for overlapping features between two BED files	C++
ComplementBED	Complement BED file	C++
CoverageBED	Coverage in second BED from first	C++
CSVCat	Concatenate two CSVs	Python
CSVCoarseFine	Coarse and fine level CSV summations	Python
CSVCol	Extract columns from CSV	Python
CSVColumnQuote	Quote columns of CSV	Python
CSVCrack	Crack open a CSV (remove borders)	Python
CSVHead	Head of every CSV row	Python
CSVMap	Map bacterial names in CSV file	Python
CSVReplace	Take a CSV file, and replace one value by another	Python
CSVSmooth	Smooth filtered CSVs	Python
CSVSubtract	Subtract the contents of two CSV files	Python
ChangeLevel	Change phylogenetic analysis level	R
CLR	Center Log Ratio (CLR) transformation	R
CombineAbundance	Combine abundances from multiple samples	Python
Copy	Make a copy of a file	Python
CSVAppend	Append a new row or column to a CSV file	Python
CSVCollate	Collate a set of CSV files into one	Python
CSVComma	Pad CSV with comma	Python
CSVJoin	Database join	Python
CSVJoinSplit	Generate taxonomically classified taxa counts from original counts, metadata and taxonomic tree	R
CSVLabel	Label rows of a CSV file	Python
CSVLast2First	Move the last column of a CSV file to the first	Python
CSVMapRange	Map Range of One CSV File To Another (Useful in Multi-Omics)	Python
CSVMerge	Merge Multiple CSV Files	Python
CSVMult	Multiply a CSV file by a constant	Python
CSVNormalize	CSV Normalization	Python
CSVPad	CSV Padding	Python
CSVPool	Take a CSV and pool together duplicate rows/columns	Python
CSVQuote	Add quotes to row and column headers	Python
CSVRemoveQuotedCommas	Remove commas from inside quoted strings in CSV file	Python
CSVRename	Rename rows and/or columns of a CSV	Python
CSVScale	Scale CSV Values to Have a Median of One	Python
CSVSort	Sort a CSV file by row	Python
CSVTranspose	Transpose a Matrix in a CSV File	Python
CSVUnNormalize	CSV Reverse Normalization	Python
CSVUnPad	Remove CSV padding	Python
CSVUnQuote	Remove quotes from CSV file	Python
CSVZero2Min	Change All Zeroes in a CSV to the Minimum Value	Python
CreateGroupings	Create groupings for a dataset	Python
DBUnroll	Unroll a database	Python
Dereplication	Convert redundant reads into sequences and counts	R
DGEList	Convert input to DGEList format	R
DNA2Protein	Corresponding protein for DNA sequence	Python
DNAComplement	Complement a DNA sequence	Python
DNAReverseComplement	Reverse complement a DNA sequence	Python
FASTACat	Concatenate FASTA files	Python
FASTAClean	Remove metacharacters from FASTA headers	Python
FASTAEven	Even lines of FASTA file	C++
FASTAREGEX	Search FASTA for regular expression	Perl
FASTAReplace	Replace sequence names with OTU	Python
FASTAShard	Split a FASTA file into shards	Python
FASTQContig	Split FASTQ file into contigs	C++
GMLMap	Map bacterial names in GML file	Python
GeneUnify	Unify gene expression values across multiple files	R
Head	Top n entries (typically of a feature list)	R
Hellinger	Hellinger transform (Hellinger et al, 1914)	R
IDXShard	Split an index into shards	C++
IntersectBED	Intersect two BED files	C++
IRLBA	Fast truncated SVD	R
KronaReplace	Replace a string in a Krona file by another string	Python
LEfSeKeepUnique	Keep only unique taxa in LEfSe input	Python
LEfSeUnClassified	Rename unclassified taxonomies	Python
LabelDups	Take a CSV file and label duplicate entries	Python
Linear	Linear model fit	R
LinksBED	Lookup known gene in UCSC browser	C++
Log1P	Transform data by log(1)	R
Log10	Transform data by log base 10	R
Log10P	Transform data by log(1+x)	R
LogTransform	Log-transform data	Python
Map2Positive	Map All Edges To Positive Range	Python
MaskFASTAFromBED	Mask FASTA based on BED intervals	C++
MergeBED	Merge BED files	C++
MergeFiles	Merge the content of all files that match a pattern	Python
MergePairedEnd	Merge paired-end reads	R
MergeSRA	Merge FASTQ files listed in an SRA input	Python
MetaPrefix	Metadata based on prefix	Python
MetabNorm	Mixed-Mode (Cohort and Batch) Metabolite Normalization (Jauhiainen et al, 2014)	R
MetaPhlAnSplit	Split MetaPhlAn (Beghini et al, 2021) taxonomy into phylogenetic classifications	Python
NewickFixAdjacent	Fix adjacent nodes of Newick tree	Python
NOAMap	Map bacterial names in NOA file	Python
NormScoreTransform	Normal Probability Values	R
Oksanen	Oksanen transformation (Oksanen, 1983)	R
Overlap	Amount of overlap between BED and genome	C++
ParseUnique	Output unique bacteria	Perl
Permute	Permute taxa abundances	Python
PhyloSeqMark	Take PhyloSeq (McMurdie and Holmes, 2013) and mark elements	Python
PhyloSeqMerge	Merge PhyloSeq (McMurdie and Holmes, 2013) data	Python
PhyloSeqNAResolve	Take PhyloSeq (McMurdie and Holmes, 2013) taxonomy table and resolve all unclassifiable levels	Python
PhyloSeqNormalize	Normalize PhyloSeq (McMurdie and Holmes, 2013) taxa	Python
PhyloSeqRemoveNull	Remove null character from PhyloSeq (McMurdie et al, 2013) data	C++
PhyloSeqReorder	Reorder PhyloSeq (McMurdie and Holmes, 2013) taxa to correspond to metadata	Python
PreprocessClinical	Clinical data preprocessor	Python
Rank	Converts a set of counts to ranks in a sample	Python
Rank2Tax	Convert header of PhyloSeq (McMurdie et al, 2013) taxonomy table to use phylogeny	Python
RDPChop	Split an RDP (Cole et al, 2014) database	Perl
RemoveBothTails	Remove tails of FASTA sequences	Python
RemoveHeader	Remove header from CSV	Python
RemovePrimer	Remove primers (Quince et al, 2011)	C++
SAMMerge	Merge SAM paired-end reads	Perl
SampleExtract	Extract sample names from FASTQ files	Python
ScaleCenter	Scale and center the data	R
SeparateGroups	Separate samples into groups	Python
ShortenNames	Shorten bacterial names	Python
SlopBED	Slop a fixed number of bases	C++
SortBED	Sort a BED file	C++
SortForwardReverse	Sort forward and reverse reads to be in the same order	Python
SortSamples	Sort a set of samples by a property	Python
SortWithTemp	Sort FASTA with intermediate temporary	C++
SplitBIOM	Take a BIOM File and split it into each taxonomic tree level	Python
SplitByLineCount	Split FASTA by line count	Python
SplitTableProcessing	Take a table of counts from Mothur and split into multiple counts classified by taxonomy	Python
StandardScaler	StandardScaler (Raju et al, 2020) normalization	Python
SubtractBED	Subtract a second BED from the first	C++
Standardize	Transform to standard distribution	R
TAB5Shard	Split a TAB5 file into shards	Python
TSV2KEGG	Convert KEGG identifiers to pathway names	Python
TSVRemove	Remove rows and columns from TSV file	Python
TaxonomySplit	Take a table of abundances and make multiple, one for each level of the taxonomic tree	Python
Transform	Shift composition (Egozcue and Pawlowski-Glahn, 2016)	Python
TSVPerturb	Perturb values in TSV file	Python
VST	Standardized values	R
WindowBED	Find features in BED within a window	C++
Z	Z-transformation	R
Zero2One	Perturb zeroes to ones	Python

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