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farhat-lab / gentb-site

The genTB project, the Django site, variant calling and prediciton pipeline, and mapping pipeline with hooks to two ravens
https://gentb.hms.harvard.edu
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Setting aligner minimap2 to short-read mode with prior paired fastq check #217

Closed mgro closed 3 years ago

mgro commented 3 years ago

Minimap2 is currently not run in short-read mode. Current command is minimap2 -a, short-read mode that takes paired read information into account minimap2 -ax sr.

Before changing this it would be necessary to ensure paired fastq files are in the same order and are exact matches (i.e., each read identifier in the first fastq file has its exact matched pair in the second fastq file).

There is a script from BBMap that does exactly this. It can be called as follows:

repair.sh in1=fastq1.fq in2=fastq2 out1=fixed1.fq out2=fixed2.fq outs=singletons.fq repair

mahafarhat commented 3 years ago

ok we discussed this and we just need to change minimap2 -ax sr and do some testing. @mgro please close this issue when its complete.

mahafarhat commented 3 years ago

OK this is now implemented.