Releases: fmalmeida/MpGAP
fmalmeida/MpGAP v2.3.1
The pipeline
MpGAP, is a very customisable (easy to use) pipeline that uses state-of-the-art software for the assembly of sequencing reads. It is capable of performing short-reads-only, long-reads-only and hybrid assemblies using data from Illumina, Pacbio and Oxford Nanopore Technologies sequencing platforms. As a plus, is has only Docker and Nextflow as dependencies.
Relase notes
In summary, this patch release improves the CLI help messages and improves how shovill is being used. The notes can be checked in the CHANGELOG.md.
fmalmeida/MpGAP v2.3
The pipeline
MpGAP, is a very customisable (easy to use) pipeline that uses state-of-the-art software for the assembly of sequencing reads. It is capable of performing short-reads-only, long-reads-only and hybrid assemblies using data from Illumina, Pacbio and Oxford Nanopore Technologies sequencing platforms. As a plus, is has only Docker and Nextflow as dependencies.
Version
In summary, this version marks the addition of new assemblers, of the param --prefix and text file summarizing assembly statistics that can be read in terminal. The latest changes applied from version 2.2 to 2.3 are described in the CHANGELOG.md file.
fmalmeida/MpGAP v2.2
The pipeline
MpGAP, is a very customisable (easy to use) pipeline that uses state-of-the-art software for the assembly of sequencing reads. It is capable of performing short-reads-only, long-reads-only and hybrid assemblies using data from Illumina, Pacbio and Oxford Nanopore Technologies sequencing platforms. As a plus, is has only Docker and Nextflow as dependencies.
Version
The latest changes applied from version 2.1 to 2.2 are described in the CHANGELOG.md file.
fmalmeida/MpGAP v2.1
The pipeline
MpGAP, is a very customisable (easy to use) pipeline that uses state-of-the-art software for the assembly of sequencing reads. It is capable of performing short-reads-only, long-reads-only and hybrid assemblies using data from Illumina, Pacbio and Oxford Nanopore Technologies sequencing platforms. As a plus, is has only Docker and Nextflow as dependencies.
Version
The latest changes applied from version 2.0 to 2.1 are described in the CHANGELOG.md file. From this version forward, everything will be documented there.
fmalmeida/MpGAP v2.0
About
This pipeline is able to assemble genomes using data from Pacbio, ONT and Illumina, in longreads-only, illumina-only or hybrid modes. It has been mainly tested in bacterial genomes but, theoretically, it can be used for other data since only Unicycler assembler is specific for prokaryotes.
Changes
- This version marks the change from nextflow DSL 1 to DSL 2
- The two hybrid strategies have been separated by the use of
--illumina_polish_longreads_contigsparameter - It is now possible to polish nanopore assemblies with Medaka or Nanopolish
- A known bug with Unicycler when using unpaired + paired end reads have been fixed
- Docker images and config files have been updated
fmalmeida/MpGAP v1.1
About
This pipeline is able to assemble genomes using data from Pacbio, ONT and Illumina, in longreads-only, illumina-only or hybrid modes.
It has been mainly tested in bacterial genomes but, theoretically, it can be used for other data since only Unicycler assembler is specific for prokaryotes.
Changes
In this release we added some minor updates in order to try to make it easier to use Nanopolish since we were having some problems with the nomenclature while giving parameters
Also, we have fixed some inconsistencies in the documentation
fmalmeida/MpGAP v1.0
This pipeline is able to assemble genomes using data from Pacbio, ONT and Illumina, in longreads-only, illumina-only or hybrid modes.
It has been mainly tested in bacterial genomes but, theoretically, it can be used for other data since only Unicycler assembler is specific for prokaryotes.