postprocessing: QC
After preprocessing with IMP3
, run additional QC steps:
-
fastqc
,multiqc
-
number of reads: raw (R1, R2), processed (R1, R2, SE), SARS-CoV-2 (R1, R2) -
kraken2
for (PhiX)/host -
fastv
for SARS-CoV-2 -
fastv
for viruses -
for SARS-CoV-2 (incl. also some other viruses)pacific
- pacific issue 8
- relat. high runtime thus limiting to MT only
-
mash
for sample (dis)similarity estimation- issue 164 - waiting
-
for sample (dis)similarity estimationsourmash
- requires FASTQ preprocessing