v2.0.0

In this new version, Mapler now anlyses the alignment of reads on contigs, with the aligned read ratio and aligned base ratio metrics. It also uses this alignment to separately analyse reads that were successfully assembled (aligned to the assembly) and reads that were not, with FastQC , KAT and Kraken2. It also taxonomically assigns bins with GTDB-Tk. Several tools were updated, notably upgrading CheckM to CheckM2.

Support for non-HiFi long reads has been deprecated, but the pipeline now accepts compressed reads as input. Installation has been streamlined with automatic dependency installation, an improved documentation and a test dataset.

Mapler now saves logs in a dedicated logfile, for a better traceability. Several bugs have been fixed.

v1.1.0

Implementation of hybrid assembly with Opera-MS.
Works on Plafrim, untested on Genouest
Assembly functional, haven't tested compatibility with evaluation metrics

v1.0.0

First stable version, with support for 3 assemblers, and assembly of hi-fi and lo-fi long reads, and three kinds of evaluation metrics

v0.0.0

Unstable version, for archiving before reworking the pipeline