v0.3.2

Version v0.3.x of the pipeline is compatible with the descriptions and data in:
SM Karst, RM Ziels, RH Kirkegaard, EA Sørensen, D. McDonald, Q Zhu, R Knight, & M Albertsen. (2020). Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. bioRxiv, 6459039.

Bug fixes

• Re-introduce Racon window trimming for pacbio_pipeline. No trimming results in higher error rate.

Minor changes

• Updated readme and example analysis.

v0.3.1

Version v0.3.x of the pipeline is compatible with the descriptions and data in:
SM Karst, RM Ziels, RH Kirkegaard, EA Sørensen, D. McDonald, Q Zhu, R Knight, & M Albertsen. (2020). Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. bioRxiv, 6459039.

Bug fixes

• Disabled end trimming in Racon, which resulted in truncated UMI consensus sequences. Truncation in some cases resulted in removal of priming sites and the sequences being discarded.
• UMI cluster size was underestimated by 50% due to mapping settings discarding reverse complement matches. The impact was mainly on low abundant UMI bins, which is primarily relevant for PacBio CCS data.

Major changes

• Filtering of poor UMI bins by UMI match error, UMI bin size/cluster size ratio and read orientation ratio was integrated into the UMI binning step.

Minor changes

• Updated readme and example analysis.

v0.3.0

Version v0.3.x of the pipeline is compatible with the descriptions and data in:
SM Karst, RM Ziels, RH Kirkegaard, EA Sørensen, D. McDonald, Q Zhu, R Knight, & M Albertsen. (2020). Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. bioRxiv, 6459039.

Major changes

• Conda installation now an option and recommended.
• PacBio pipeline added.
• longread_umi pipelines and tools can now be accessed by just calling longread_umi <tool/pipeline>
• Demultiplexing scripts and a barcode template script have been added for custom primer/adaptor demultiplexing.
• Readme streamlined, usage added and example data/analysis added along.
• R functions for data validation was added.
• umi_binning was tuned to better find low coverage UMIs

Minor changes

• Pipeline name simplified to longread_umi from longread-UMI-pipeline
• polish_medaka speed optimization and better control of parallel jobs.
• qc_pipeline streamlining and more stats.
• primer_position updated to provide adapter positions as well.
• trim_amplicon updated to work with custom primers.
• variants now dereplicates before clustering and uses centroids as cluster mapping reference.
• Zymomock rRNA reference sequences was updated to remove indel error in Salmonella reference.

v0.2.1

Minor improvements

• Implemented conda installation
• Streamlined instructions
• GNU parallel --env for more robust function export

Minor fixes

• Updated Zymo mock references (1 indel error).

Version v0.2.x of the pipeline is compatible with the descriptions and data in:
Karst, S. M., Ziels, R. M., Kirkegaard, R. H., & Albertsen, M. (2019). Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers and Nanopore sequencing. bioRxiv, 645903.
https://www.biorxiv.org/content/10.1101/645903v2