Name	Short Description	Language
Abund2LEfSe	Convert abundances to LEfSe format	Python
Abund2XML	Convert abundances to XML	Python
AbundCSV2NOA	Convert CSV file of abundances to NOA for Cytoscape	Python
Any2FASTA	Convert one of several formats to FASTA	C++
BAM2BED	Convert BAM input to equivalent BED	C++
BAM2FASTQ	Convert BAM input to equivalent FASTQ	C++
BAM2SAM	Convert BAM input to equivalent SAM	C++
BED122BED6	Convert BED v12 to BED v6	C++
BED2BAM	Convert BED input to equivalent BAM	C++
BED2FASTA	Convert BED to FASTA	Python
BED2IGV	Convert BED input to IGV	C++
BED2Junc	Convert BED to Junc	Perl
BIOM2CSV	Convert BIOM file to CSVA	Python
BIOM2Upgrade	Convert to BIOM2 format	Python
BLAST2Tab	Convert BLAST output to tabular format	Perl
BWA2Bowtie	Convert BWA file to Bowtie compatible input	C++
Bowtie2Abund	Extract abundances from Bowtie2 (Langmead et al, 2012)	Python
CSV2LEfSe	Convert CSV abundance and metadata to LEfSe input	Python
ClusterCSV2NOA	Convert CSV File Of Clusters to NOA	Python
CountTableProcessing	Converts Mothur Counts To Abundance CSV	R
CSV2Dot	Take a Network in CSV Format and Visualize in Dot (Gansner et al, 2015)	Python
CSV2EDA	Converter from CSV to Cytoscape EDA file format	Python
CSV2GML	CSV To GML Converter	Python
CSV2PLSDA	Convert an input CSV file to multiple files that can be analyzed with PLSDA (Stahle and Wold 1987)	Python
CSV2PathwayTools	Take a CSV file and perform lookups in PathwayTools (Karp et al, 2015)	Python
CSV2QZA	Convert a CSV to Qiime2 (Bolyen et al, 2019) QZA file	C++
CSV2TSNE	Convert CSV file of abundances to multiple input files for TSNE (Van der Maaten et al, 2008)	Python
CSV2TSV	Converter from comma-separated to tab-delimited format	Python
DESeq2TXT	Human-readable statistics for DESeq2 (Love et al, 2014) output	Python
FASTA2FA	FASTA to FA file	Python
FASTA2FASTQ	Convert from FASTA to FASTQ format	Python
FASTQ2454	Convert from FASTQ to 454 format	Perl
FASTA2Phylip	Convert from FASTA to Phylip format	Perl
FASTQ2FASTA	Convert from FASTQ to FASTA format	Python
FASTQ2QZA	Convert a group of FASTQ files to Qiime2 (Bolyen et al, 2019) QZA (Generated by PluGen)	C++
FASTQ2TAB5	Convert from FASTQ to TAB5 format	Python
FASTQRandom	Generate random FASTQ file	C++
FixMegaHitContig	Convert MegaHit contigs (Uritsky et al, 2018)	Python
FlatFile	Flat file from FASTA	Perl
GB2CSV	GenBank To CSV Converter	Python
GML2CSV	GML To CSV Converter	Python
GML2GraphML	Convert GML to GraphML format	Python
GTF2BED	Convert GTF file to BED	C++
GTF2CSV	GTF to CSV Converter (Xue, 2021)	C++
Gunzip	Extract a GZ	C++
HMDB2KEGG	Convert HMDB identifiers to KEGG	Python
Harvest	Harvest (Treagen et al, 2014) tools	C++
HeterogeneousXML	XML file for heterogeneous network	R
Hours	Take a data file and accumulate hourly	Python
Kaiju2Krona	Conver Kaiju input to Krona	Python
Kaiju2Table	Convert Kaiju input to table	Python
Kraken2Krona	Convert Kraken to Krona plot (Uritsky et al, 2018)	Python
Kraken2MPA	Convert Kraken output to MPA format	Python
Kraken2Translate	Convert Krak2 to Kraken2 (Uritsky et al, 2018)	Python
Krona2CSV	Convert a Krona file to multiple CSV files, one per taxonomic level	Python
Krona2PhyloSeq	Convert a Krona file to PhyloSeq (McMurdie et al, 2013) OTU and taxonomy tables	Python
KronaGram	Make KronaGram (Uritsky et al, 2018)	Python
KronaTree	Convert a Krona file to multiple TXT files, one per taxonomic level	Python
MetaPhlAn2LEfSe	Convert MetaPhlAn abundances to LEfSe format	Python
Mothur2PhyloSeq	Convert Mothur (Schloss et al, 2009) output to PhyloSeq (McMurdie and Holmes, 2013) input	R
NCBI2Newick	Convert NCBI IDs to Newick tree	Python
PathwayTools2HMDB	Map PathwayTools (Karp et al, 2015) identifiers to HMDB	Python
PCL2CSV	PCL To CSV (File Conversion)	Python
PCPoints	Convert principal components to (x,y) coordinates	Python
PhyloSeq2CSV	Convert PhyloSeq (McMurdie et al, 2013) data to CSV format	R
PhyloSeq2LEfSe	Convert PhyloSeq (McMurdie and Holmes, 2013) data to a single file that can be analyzed by LEfSe (Segata et al, 2011) for biomarkers	R
PhyloSeq2Qiime	Convert PhyloSeq (McMurdie and Holmes, 2013) data files (OTU/TAX/META) into Qiime (Caporaso et al, 2010)-compatible (BIOM/TRE) formats	R
Qiime2Export	Export a Qiime2 (Bolyen et al, 2019) QZA file	C++
Qiime2PhyloSeq	Convert Qiime (Caporaso et al, 2010) OTU and metadata files to PhyloSeq (McMurdie and Holmes, 2013) format	Python
Qiime2Tree	Convert a Qiime2 (Bolyen et al, 2019) QZA file of sequences to a phylogenetic tree	C++
QiimeMetadataTranslate	Convert CSV file of metadata to Qiime1/Qiime2	Python
QiimeTwo2PhyloSeq	Convert input files from Qiime2 (Bolyen et al, 2019) to PhyloSeq (McMurdie et al, 2013)	R
SAM2BAM	Convert SAM to BAM	C++
SAM2BED	Convert SAM to BED	Perl
SAV2CSV	Convert SAV to CSV	R
Sanger2Illumina	Convert Sanger sequences to Illumina format	Perl
SIF2CSV	SIF To CSV (Interactions to Correlations)	Python
SRX2SRA	SRX identifiers to SRA	Python
SSV2CSV	Convert a semicolon-separated value (SSV) file to comma-separated (CSV)	Python
Tax4Fun2LEfSe	Convert Tax4Fun2 (Wemheuer et al, 2020) output to LEfSe input format (Segata et al, 2011)	Python
TSV2CSV	Converter from tab-delimited to comma-separated format	Python
Tab2GML	Converter from tab-delimited to GML format	Python
Tax4Fun2LEfSe	Convert Tax4Fun format to LEfSe	Python
TaxID2Lineage	Obtain lineage from taxonomic identifiers	Python
TSV2BIOM	Convert a tab-separated file to BIOM format	Python
TX2SG	Convert transcripts to splice graph	R
Uniq2FASTA	Convert unique sequences to FASTA format	Python

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