From: Wochenende — modular and flexible alignment-based shotgun metagenome analysis
Function | Tool | Reference |
---|---|---|
Tool packaging | Bioconda | [7] |
Quality control | FastQC | [8] |
MultiQC | [9] | |
Prinseq | [10] | |
Trimming | Fastp | |
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] |