Abstract
The MinION sequencer by Oxford Nanopore Technologies turns DNA and RNA sequencing into a routine task in biology laboratories or in field research. For downstream analysis it is required to have a sufficient amount of target reads. Especially prokaryotic or bacteriophagic sequencing samples can contain a significant amount of off-target sequences in the processed sample, stemming from human DNA/RNA contamination, insufficient rRNA depletion, or remaining DNA/RNA from other organisms (e.g. host organism from bacteriophage cultivation). Such impurity, contamination and off-targets (ICOs) block read capacity, requiring to sequence deeper. In comparison to second-generation sequencing, MinION sequencing allows to reuse its chip after a (partial) run. This allows further usage of the same chip with more sample, even after adjusting the library preparation to reduce ICOs. The earlier a sample's ICOs are detected, the better the sequencing chip can be conserved for future use. Here we present sequ into, a low-resource and user-friendly cross-platform tool to detect ICO sequences from a predefined ICO database in samples early during a MinION sequencing run. The data provided by sequ-into empowers the user to quickly take action to preserve sample material and chip capacity. sequ-into is available from https://github.com/mjoppich/sequ-into .
| Dokumententyp: | Zeitschriftenartikel |
|---|---|
| Fakultät: | Medizin
Mathematik, Informatik und Statistik > Informatik |
| Themengebiete: | 600 Technik, Medizin, angewandte Wissenschaften > 610 Medizin und Gesundheit
000 Informatik, Informationswissenschaft, allgemeine Werke > 004 Informatik |
| ISSN: | 2001-0370 |
| Sprache: | Englisch |
| Dokumenten ID: | 84798 |
| Datum der Veröffentlichung auf Open Access LMU: | 25. Jan. 2022, 09:11 |
| Letzte Änderungen: | 25. Jan. 2022, 09:11 |
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