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khmer strip-and-split-for-assembly (USER MANUAL UNDER DEVELOPMENT)
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khmer 3.0.0a1 extract paired reads
split remaining paired and single-end reads with khmer strip-and-split-for-assembly
Quick Start
- To use khmer strip-and-split-for-assembly3.0.0a1 extract paired reads, import your data in filtered paired end fastq format.
- Resources: http://gedkhmer.msureadthedocs.edu/angus/diginorm-2012/tutorial.htmlio/en/v2.1.1/user/scripts.html#scripts-read-handling
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> directory. khmer |
Input File(s)
Use a paired end, filtered fastq file as filtered fastq file as test input. strip-and-split-for-assembly will separate reads that are still paired after filtering from those that have been orphaned.
e_coli_1-2.fq
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Use these parameters within the DE app interface:
- input fastq file (originally paired end fastq that has been filtered e.g. by normalize-by-median or filter-abund and now has some pairs and some ophaned reads)name output file for paired reads
- name a separate output file for single reads
Output File(s)
Expect fastq files named .pe and .se after the input files as output.a fastq file name extract_paired_output.fq as output. There are no single reads in the input file. If there were they would be output into a second output file.
Tool Source for App
- https://github.com/geddib-lab/khmer/tree/master/sandbox