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This artifact may be resolved by re-running a Markov chain after each merge using the newly obtained model, which will allow to re-estimate the posterior variance-covariance matrices needed to predict the next merge operation.
After using the DQer to break up contigs consisting of more than 10% questionable clones, a consecutive reduction in stringency at 1e-5 for each End-End and Single-End merge using the "clone plus markers (CPM)" function at a tolerance of 3 was performed to reassemble contigs.
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These annotations were merged using the Cuffmerge algorithm to obtain the reference annotation for further analysis55.
Raw sequence reads were quality filtered using Trimmomatic and paired end reads were merged using the software PEAR.
To further reduce sequencing errors, sequences that were within 2 bp of a more abundant sequence were merged using the pre.cluster command.
Then, the three assemblies were merged using the HABOT2 (hybrid assembly of third-generation sequencing 2; https://github.com/asarum/HABOT2) software (1gene Corp., Hangzhou, China).
The database is structured in three independent files that can be merged using the code identifier for the provenance and the code combining the trial and provenance codes ("Trial" and "ID_ProvCode", respectively).
Following [27], samples located in the same ROI were merged using the mean statistics.
Images were captured using a digital camera at 40× magnification and merged using the IAS2000 software.
The images were merged using the SimplePCI software (C-IMAGING, PA, USA).
Three images were processed and merged using the MRC package [53].
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