Automated composition of the Cascabel Pipeline

Cascabel (https://doi.org/10.3389/fgene.2020.489357) is a variable pipeline for amplicon sequence data analysis.

It makes an interesting use case for workflow work with bio.tools/EDAM and APE, as it already foresees several variants of the main workflow, and potentially more can be found when taking to account the full content of bio.tools.

Notes

Takes raw data as input and delivers a table of operational taxonomic units (OTUs) or Amplicon Sequence Variants (ASVs) in BIOM and text format and representative sequences.

• For inputs and outputs: type (comma separated formats).
• ⁿ : Could not be found in bio.tools, based on context from Cascabel or other source.

Tool	in bio.tools	ID	Inputs	Outputs
Minimum entropy Decomposition (MED)	No	-	-	-
Swarm	Yes	biotools:swarm	Nucleic acid sequence (FASTA-like)	Sequence cluster (Textual format)
DADA2	Yes	biotools:dada2	Demultiplexed FASTQ files9	Sequence variants9
deblur	No	-	-	-
QIIME	Yes	biotools:qiime	Raw sequence6	-
QIIME 2.0	Yes	biotools:qiime2	Raw sequence6	-
mothur	No	-	Sequence13 (FASTA)13	Taxonomy summary12 (Sequence feature annotation format)13
VSEARCH	Yes	biotools:vsearch	Nucleic acid sequence (FASTQ16)	Sequence similarity score, sequence alignment
FastQC	Yes	biotools:fastqc	Raw sequence (FASTQ-like format (text), SAM, FASTQ, BAM)	Sequence report (HTML)
PEAR	Yes	biotools:pear	-	Sequence assembly5
Cutadapt	Yes	biotools:cutadapt	RNA sequence (FASTQ, FASTA)	RNA sequence (FASTQ, FASTA)
Cutadapt 1.12	Yes	biotools:cutadapt_1.12	RNA sequence (FASTQ, FASTA)4	RNA sequence (FASTQ, FASTA)4
SortMeRna	Yes	biotools:sortmerna	(FASTA, FASTQ), RNA database14	-
trie	No	-	-	-
UCLUST	No	-	Sequence (FASTA, FASTQ)2	-
UCLUST_REF	No	-	-	-
USEARCH	Yes	biotools:usearch	Sequence (FASTA, FASTQ)1	Sequence (FASTA, FASTQ)1
USEARCH_REF	No	-	-	-
CD-HIT	Yes	biotools:cd-hit	Sequence alignment (FASTA)	Data (Textual format), Data (Textual format), Sequence alignment (FASTA)
SUMACLUST	No	-	Sequence3	-
BLAST	No	-	Sequence15 (FASTA)17	Statistical estimate score15 (HTML, XML, JSON, Textual format)17
BLAST+	No	-	Sequence15 (FASTA)17	Statistical estimate score15 (HTML, XML, JSON, Textual format)17
pynast	No	-	-	-
MAFFT	Yes	biotools:MAFFT	Sequence (FASTA)	Sequence alignment (FASTA)
Infernal	Yes	biotools:infernal	Sequence profile (Sequence profile format)	Database search results
ClustalW (BioLib)	Yes	biotools:clustalw_biolib	Sequence (FASTA)	Sequence alignment (ClustalW format, FASTA, nexus-seqm, PHYLIP format)
ClustalW (PBIL)	Yes	biotools:clustalw_pbil	Sequence (FASTA)	Sequence alignment (FASTA)
ClustalW (SIB)	No	-	Sequence (FASTA)	Sequence alignment (FASTA)
RAxML	Yes	biotools:raxml	Phylogenetic tree8	-
FastTree	Yes	biotools:fasttree	-	Phylogenetic tree7
Krona	Yes	biotools:krona	(XML, Textual format)11	(HTML)10
SILVAngs	Yes	biotools:silvangs	Nucleic acid sequence (FASTA)	Nucleic acid sequence (FASTA), Matrix (TSV), Plot, Report (PDF), Sequence cluster nucleic acid (FASTA), Nucleic acid sequence (Binary format)
MG-RAST	Yes	biotools:mg-rast	-	-
NGTax2	No	-	-	-
SLIM	Yes	biotools:SLIM	-	-

1. drive5.com
2. drive5.com
3. Sumaclust Wiki
4. Does not have inputs and outputs in bio.tools. Is based on other Cutadapt. Note: according to bio.tools, Cutadapt is a "Sequence trimming" operation while Cutadapt 1.12 "Data handling". "Sequence trimming" being more specific.
5. Based on PEAR documentation.
6. Based on QIIME's description on bio.tools.
7. Based on FastTree's description on bio.tools.
8. Based on FastTree manual.
9. Based on DADA2's description on bio.tools.
10. Based on Krona's description on bio.tools.
11. Based on Krona's wiki on GitHub.
12. Based on mothur_krona's description on bio.tools.
13. As described by mothur's manual.
14. As described by SortMeRna's website.
15. As described by BLAST's website.
16. Supports at least FASTQ format according to VSEARCH's bio.tools.
17. As described by BLAST's API documentation.