Filter and map reads module
This module combine in one module in Hadoop mode the filtering of the reads, the mapping and the filtering of the alignments. This module only is available in hadoop mode is more efficient than using the 3 steps successively.
- Internal name: filterandmap
- Available: Distributed mode only
- Input ports:
- reads: reads in FASTQ format (format: reads_fastq)
- mapperindex: mapper index for the genome (automatically generated from genome sequence file)
- genomedescription: genome description (automatically generated from genome sequence file)
- Output port:
- output: alignments in FASTQ format (format: mapper_results_sam)
- Optional parameters: This module use all the optional parameters of the filterreads step, mapreads step and filtersam step. For more information, see the documentation of this steps.