SEQU-INTO : Early detection of impurities, contamination and off-targets (ICOs) in long read/MinION sequencing
© 2020 The Author(s)..
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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2020 |
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| Erschienen: |
2020 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:18 |
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| Enthalten in: |
Computational and structural biotechnology journal - 18(2020) vom: 05., Seite 1342-1351 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Joppich, Markus [VerfasserIn] |
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| Links: |
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| Themen: |
Bioinformatics |
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| Anmerkungen: |
Date Revised 11.11.2023 published: Electronic-eCollection Citation Status PubMed-not-MEDLINE |
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| doi: |
10.1016/j.csbj.2020.05.014 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM311906052 |
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| 500 | |a Citation Status PubMed-not-MEDLINE | ||
| 520 | |a © 2020 The Author(s). | ||
| 520 | |a 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 | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a Contamination | |
| 650 | 4 | |a Nanopore Sequencing | |
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| 700 | 1 | |a Olenchuk, Margaryta |e verfasserin |4 aut | |
| 700 | 1 | |a Mayer, Julia M |e verfasserin |4 aut | |
| 700 | 1 | |a Emslander, Quirin |e verfasserin |4 aut | |
| 700 | 1 | |a Jimenez-Soto, Luisa F |e verfasserin |4 aut | |
| 700 | 1 | |a Zimmer, Ralf |e verfasserin |4 aut | |
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