Wochenende — modular and flexible alignment-based shotgun metagenome analysis

BMC Genomics

Table 1 Bioinformatics tools in the Wochenende pipeline

Function	Tool	Reference
Tool packaging	Bioconda	[7]
Quality control	FastQC	[8]
	MultiQC	[9]
	Prinseq	[10]
Trimming	Fastp	[9, 11]
Trimming	Trimmomatic	[12]
Alignment	BWA-mem	[13]
	ngmlr	[14]
	minimap2	[15]
Format conversion/filtering	Samtools	[16]
	Sambamba	[17]
	Bamtools	[18]
Realignment	Abra2	[19]
Plotting	Python Matplotlib 3.2.1	[20]
Data munging	Python pandas 1.1.1	[21]
Taxonomic visualization	Metacoder	[22]

ISSN: 1471-2164