BioModules used to prepare sequence files or update the metadata prior to classification.See: Description
| Class | Description |
|---|---|
| AwkFastaConverter |
This BioModule uses awk and gzip to convert input sequence files into a decompressed fasta file format.
|
| Gunzipper |
This BioModule uses gzip to decompress input sequence files.
|
| KneadData |
This BioModule runs biobakery kneaddata program to remove contaminated DNA.
Multiple contaminent DNA databases can be used to filter reads simultaniously. Common contaminents include Human, Viral, and Plasmid DNA. |
| Multiplexer |
This BioModule will merge sequence files into a single combined sequence file, with either the sample ID or an
identifying bar-code (if defined in the metatata) is stored in the sequence header.
BioLockJ is designed to run on demultiplexed data so this must be the last module to run in its branch. |
| PearMergeReads |
This BioModule will merge forward and reverse fastq files using PEAR.
For more informations, see the online PEAR manual: https://sco.h-its.org/exelixis/web/software/pear/doc.html |
| RarefySeqs |
This BioModule imposes a minimum and/or maximum number of reads per sample.
|
| SeqFileValidator |
This BioModule validates fasta/fastq file formats are valid and enforces min/max read lengths.
|
| TrimPrimers |
This BioModule removes sequence primers from demultiplexed files.
The primers are defined using regular expressions in a separate file. |
BioModules used to prepare sequence files or update the metadata prior to classification.