This repository contains shell and python scripts for quality control of sequencing data. The scripts are designed to be used to compare the quality of sequencing data from different sequencing platforms. We compare the following vendors:
- Element Bio AVITI - downloaded from https://nextnuc.gbiomed.kuleuven.be/index.php/s/mkLgECw2odysgaL (password protected, credentials available on request) - 20241011_AV242402_4854_1-RawData-4854.tar, unpacked into /data/luka.lenaroto/eDentity/sequencer_tender/elements on MaaS 37
- Illumina - downloaded from naturalis@sftp.nrcnvwa.nl via sftp (credentials available on request) - /data/luka.lenaroto/eDentity/sequencer_tender/241008_VH00147_37_AAG3LFWM5 on MaaS 37
Total sum of *.fastq.gz file sizes: 43497579058 bytes (43.5 GB). Note that these are compressed by the vendor, and we don't know the compression ratio. Hence, this is merely a very rough estimate.
Markers in multiplexed data set according to Elements:
- Empty
- ITS-Blank
- ITSmix-Blank
- ITSmix-NL2
- ITSmix-SB
- ITS-NL2
- ITS-SB
- LSU-Blank
- LSU-NL2
- LSU-SB
- SSU-Blank
- SSU-NL2
- SSU-SB
Total sum of *.fastq.gz file sizes: 115430885055 bytes (115.4 GB). Note that these are compressed by the vendor, and we don't know the compression ratio. Hence, this is merely a very rough estimate.
Markers in multiplexed data set according to Illumina:
- Empty
- ITS-Blank1
- ITS-Blank2
- ITS-Blank3
- ITSmix-Blank1
- ITSmix-Blank2
- ITSmix-Blank3
- ITSmix-NL2
- ITSmix-SB
- ITS-NL2
- ITS-SB
- LSU-Blank1
- LSU-Blank2
- LSU-Blank3
- LSU-NL2
- LSU-SB
- SSU-Blank1
- SSU-Blank2
- SSU-Blank3
- SSU-NL2
- SSU-SB
- Undetermined
Intermediate results are stored in the results folder.