How to deal with paired-end sequencing file

medvir / SmaltAlign

Quick iterative alignment of reads against a given reference using smalt.

MIT License

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How to deal with paired-end sequencing file #12

Closed rongfengchen closed 1 year ago

rongfengchen commented 1 year ago

For Illumina sequencing, we have R1 and R2 fastq files for one sample? How to deal with these paired-end sequencing file? Should I merge R1 and R2 first, then use SmaltAlign to do align?

MaryamZaheri commented 1 year ago

If the paired-end reads overlap you can use tools such as PEAR to merge the reads. Otherwise you can just concat all reads in one file and use the tool.