Releases: jtamames/SqueezeMeta
Releases · jtamames/SqueezeMeta
Release list
v0.4.3
Minor changes
- We now provide a pre-compiled version of the database, which can be downloaded via the script
.../SqueezeMeta/scripts/preparing_databases/download_databases.pl <datapath>. This is quicker and safer against changes in NCBI. - Removed dependency on bedtools.
v0.4.2
Announcement
- The latest NCBI nr release didn't play nice with our parser. In particular, one of the new entries led to the appearance of unclosed quotes in an intermediate file, which in turn led to SQLite not parsing the file from that point on. As a result, taxonomic annotation was far more scarce that it should be. Those of you that have been experiencing troubles and downloaded the database in the last month might want to re-build it using the scripts provided in this version, which fix that particular problem. We'll keep improving our parser so that issues like that become as infrequent as possible. Meanwhile, please smash that issue button if you find that something is not working as intended!
New features
- SqueezeMeta does now work in CentOS7, in addition to Ubuntu14+. All necessary dependencies and installation instructions are listed in the INSTALL-CENTOS7 file.
Minor changes / Bug fixes
- Removed dependency on GCC5.
- Fixed an issue in which a recently-added entry in the NCBI nr database resulted in our LCA database being only partially created.
- Added extra checks in the make_databases.pl script to ensure that the LCA SQLite database has the same number of rows as its plain text source file.
v0.4.1
Christmas announcement
- We've started working on an installation guide for CentOS 7. Stay tuned!
Minor changes / Bug fixes
- Contigs with no proteins are now included in the 19.*.contigtable file.
- Fixed a bug occurring in newer versions of Perl (such as the one shipped with Ubuntu 18).
- Fixed a bug in which CheckM was called incorrectly with bins assigned to Candidatus genera.
- Fixed a minor bug when calculating the best average functional assignment for orfs.
v0.4.0
New features
- Changed name from SqueezeM to SqueezeMeta
- Full support for long reads (MinION, PacBio) through canu and minimap2
- Inclusion of DAS_tool for integrating the binning results of MaxBin and MetaBAT
- Control diamond memory usage via the -b parameter
Minor changes / Bug fixes
- Default minimum contig length is now 200 instead of 1200
- SqueezeMeta.pl and restart.pl should now be much more consistent at stopping whenever an intermediate step fails, and display more informative error messages
- Contig/bin "chimerism" is now called "disparity" instead
- Fixed a bug in which the latest release of nr wasn't being properly parched during database creation
- Fixed a bug in which some ORFs had an incomplete taxonomic annotation
- Fixed a bug in which many ORFs were being ignored when running MinPath
- Fixed some unfrequent bugs when using the merged mode on uncompressed files or single-end reads
- Unmapped reads now count towards the total in rpkm normalization
v0.3.1
v0.3.0
New features:
- Two new read mappers (bwa and minimap2) can be selected using the -map parameter when calling squeezeM. Minimap2 can be run in three different modes.
-- minimap2-on: for MinION reads.
-- minimap2-pb: for PacBio reads.
-- minimap2-sr: for Illumina reads. - Initial support for Oxford Nanopore MinION / PacBio reads. SqueezeM now supports the use of single-end reads. SqueezeM will treat a sample as single-end if a "pair2" is not specified for that sample in the samples file. SqueezeM now also includes an specific aligner for long reads.
- An initial implementation of the SqueezeM database and web interface can now be found in https://github.com/jtamames/SqueezeMdb.
Bug fixes:
- Fix viral taxonomy being incorrectly parsed.
- Fix a bug during database creation.
