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nf-core / bamtofastq

Converts bam or cram files to fastq format and does quality control.
https://nf-co.re/bamtofastq
MIT License
21 stars 13 forks source link

Use seqkit? #18

Open FriederikeHanssen opened 4 years ago

FriederikeHanssen commented 4 years ago

Some of the samtools steps in the beginning could possibly be replaced with seqkit pair . First do samtools fastq, then make the pairs match. Keep in mind the read order of collate though.