Du Novo: Align families
of duplex sequencing reads (Galaxy Version 2.14)Tool Parameters
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No datasets with tabular elements available
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Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the number of processes used, the time and memory taken to process it, the alignment algorithm selected, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The names of the input and output datasets are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET.
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What it does
This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads.
Input
This expects the output format of the "Make families" tool.
Output
The output is a tabular file where each line corresponds to a (single) read.
The columns are:
1: barcode (both tags)
2: tag order in barcode ("ab" or "ba")
3: read mate ("1" or "2")
4: read name
5: read sequence, aligned ("-" for gaps)
6: read quality scores, aligned (" " for gaps)
Alignments
When "MAFFT" is selected as the multiple sequence aligner, the alignments are done with the command
$ mafft --nuc --quiet family.fa > family.aligned.fa
Unnamed history
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