Parameters

Required Parameters

These can be in your nextflow config file if you wish.

• --r1 and --r2* The input reads
• --entrez_email Email to access NCBI Entrez
• --entrez_api_key API Key to access NCBI Entrez

Parameters from FastP

• --read_length
• --qualified_quality_phred
• --unqualified_percent_limit
• --length_required

Parameters from MMSeqs2

• --split_memory_limit

Additional Parameters

• --ndata Path to the SiftDx output of the negative control
• --srmode Changing the short read aligner between BLAST and MMSeqs2 (default: blast)
• --nrmode Changing the protein aligner between Diamond and MMSeqs2 (default: diamond)
• --max_read_length The cut-off for shorter vs longer reads (default: 100)
• --min_read_length The minimum read length for shorter read alignment (default: length_required)

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