v1.1.0

Major changes

• Replace Sumaclust by VSearch

v1.0.0

Major changes

• Replace ComponentSearch (java) by ComponentSearch2 (c++)

Minor changes

• Externalise conda recipe to the following repository: https://github.com/bonsai-team/conda_recipes
• Add a new option to MATAM allowing the user to run only the first step of the pipeline

v0.9.9

Minor changes

• Added conda recipe
• Corrected small bug in scaffolding step

v0.9.8

Major changes

• Contigs binning during scaffolding is now deactivated by default. This is still an experimental option.
• Updated Docker url
• Final assembly file is now explicit: "final_assembly.fa"

Minor changes

• Python sub-processes are now unbuffered
• Cleaned ovgraphbuild output
• Various cleaning and improvement to matam_assembly.py

v0.9.7

Major Changes

• Changed MATAM repository from ppericard/matam to bonsai-team/matam
• Added build clean feature [resolves #3]
• Moved Docker Hub repository to bonsaiteam/matam [resolves #13]

Minor Changes

• Clarified our policy on semantic versioning releases

v0.9.6

Minor changes

• Updated Dockerfile to use bioconda instead of some Debian packages (samtools)
• Corrected bugs
• Improved output infos
• Unix sort should now work correctly with more system configurations
• Added additional scripts

v0.9.5

Major changes

• MATAM is now compatible only with Samtools v1.x and higher

Minor changes

• Corrected bugs
• Bamtools can now be compiled with gcc-6

v0.9.4

Major changes

• Updated default DB to SILVA 128
• Default DB is now downloaded from bioinfo.lifl.fr and does not use git LFS anymore
• Added a new step to filter out references with a mapping coverage too high (most prevalent species)
• Improved Ns management during database preprocessing

Minor changes

• Corrected many bugs
• Improved output infos
• Bamtools and SGA are now compiled with the gcc version from the current user bash
• Performances improvement and better resources management
• Additional non-essential scripts

v0.9.3

Major Changes

• Cleaned and simplified ovgraphbuild code. No functional changes.
• Changed componentsearch default filtering parameters in matam_assembly.py
• matam_assembly.py now output assemblies stats at the end of the run
• Contigs assembly read correction is now an option (SGA was doing it by default) and is deactivated by default. This greatly improve assembly of low coverage species.
• Contig binning during scaffolding is now an option activated by default.
• Added options to matam_db_preprocessing.py to filter out too small or too long ref sequences

Minor Changes

• Added an option to sga_assembly.py to deactivate read correction and filtering
• Now doesnt crash if one of the assembly file is empty
• Added new script to compute fasta sequences length
• Added new script restore the .1 and .2 names to a paired fastq file missing them

v0.9.2-beta

Major changes

• Introduced compatible contigs binning in scaffolding step. This should prevent creating consensus scaffolds when contigs from 2 individuals/species map on the same reference.