New features

• Added spades-base as a possible assembler for SqueezeMeta. This will make SqueezeMeta call SPAdes with no additional flags. Flags for SPAdes can then customized by the user by passing --assembly_options "EXTRA OPTIONS" when calling SqueezeMeta. More information can be found in the ReadMe and the PDF manual.
• Added the utility script sqm2zip.py, which allows to pack the essential files from a SqueezeMeta project into a single zip file.
• SQMtools: loadSQM can now load a project directly from a zip file created by sqm2zip.py (syntax would be `loadSQM("/path/to/my_project.zip").
• SQMtools: SQMtools is now available in CRAN and can be installed with install.packages("SQMtools") in Windows, Mac and Linux computers.
• These changes are meant to allow users to easily transfer their data from their clusters/workstations to their personal computers and explore their results there.
• SQMtools: mostAbundant and mostVariable now accept the argument bycol = TRUE, which will make these functions operate on columns rather than rows.

Minor changes / bugfixes

• We now use coverage variances in addition to average contig coverages when calling metabat2, which should improve the quality of the resulting bins.
• Mapping results are now stored as BAM files instead of SAM files, which should reduce disk usage.

Known issues / Other announcements

• The make_databases.pl script may spend a lot of time in the "Creating SQLite databases" step. We have included a patch to improve this, but still it happens inconsistently (taking a few hours in some systems, and several days in others). Having a lot (1-2 Tb) of free disk space may help. download_databases.pl should be considered as the preferred way of quickly getting reasonably-up-to-date databases.
• We are discontinuing official support for CentOS7, as its default libraries are too outdated now. We plan on supporting SqueezeMeta in Debian, WSL2-Ubuntu and (hopefully) CentOS Upstream in the not so distant future.