lagoon-mcl - LAGOON-MCL v1.0.3

Homogeneity score: bug fix

- Python
Published by jroussea about 2 years ago

lagoon-mcl - LAGOON-MCL v1.0.2

Documentation: - New documentation (reStructured Text): https://github.com/jroussea/lagoon-mcl-docs - Removal of old documentation - function for checking resources - Editing the LAGOON-MCL help message

- Python
Published by jroussea about 2 years ago

lagoon-mcl - LAGOON-MCL v1.0.1

• Updated information_file.sh script. Fixed the problem that induced a Nextflow error message.
• Documentation modification
• Modification of test files
• Updated custom.config
• Add .gitignore
• Deletion of script: preparationtestdatasets.sh
• buildsingularitycontainers.sh becomes singularity_containers.sh

- Python
Published by jroussea about 2 years ago

lagoon-mcl - LAGOON-MCL v1.0.0

First release of LAGOON-MCL.

- Python
Published by jroussea about 2 years ago

lagoon-mcl - LAGOON-MCL v1.1.1

• Remove HeaderFasta module
• Update README.md
• Update documentation

- Python
Published by jroussea about 2 years ago

lagoon-mcl - LAGOON-MCL v1.1.0

A/ Modifying modules Remove unnecessary modules - RenameFastaSequences - Merge2Dataframe - Attributes - OtherAlignments - FiltrationAlignments - NetworkAddAttributes - HomogeneityScorePlot

B/ New module 1. LabelHomogeneityScore, used in conjunction with SelectLabels, to retrieve the various labels used to calculate the homogeneity score. Create a TSV file for each label. 2. PlotClusterSize (part E/ Statistics step)

C/ Sequence preparation step Modification of the sequence preparation step, It no longer creates an identifier like seq1, seq2, ... but uses the first part of the fasta sequence headers Modifying the HeaderFasta module

D/ Filtration step 1. The FiltrationAlignedItself module changes its name to FiltrationAlignments 2. Editing the filtrationalignment.py_ script => uses column position to create diamondssn.tsv_, allows you to use a pairwise alignment file that was not created by LAGOON-MCL 3. LAGOON-MCL no longer filters alignment files by percentage identity, percentage overlap and evalue. Avoid losing edges.

E/ Statics step 1. Updating the homogeneity score - input file: one TSV file per label - create a TSV file containing scores by label - no longer performs label selection: this step is performed by the LabelHomogeneityScore module 2. Updated module for creating homogeneity score graphs - create one PDF file per label 3. Module for calculating cluster size: PlotClusterSize - create a PDF file for each network, each PDF file containing a graph of the distribution of homogeneity scores

F/ Configuration files 1. Update resources.config file 2. Updating the different pipeline options => remove unnecessary options (consequences of deleting some modules) 3. Update of nextflow.config file

G/ Other information 1. Modify the organization of files and folders in the results folder 2. SeqKit is no longer used to modify fasta sequence headers 3. Removal of the Singularity container and the Conda environment containing SeqKit 4. Update README.md file 5. Documentation update

- Python
Published by jroussea about 2 years ago

lagoon-mcl - LAGOON-MCL v1.0.1

• Changed the method to convert MLC output into a TSV dataframe. Replacement of python and R scripts with a shell script (bash / awk) Allows it to be used on large datasets (several million sequences)
• Update: homogeneity score
• Update: distribution of homogeneity scores by labels

- Python
Published by jroussea about 2 years ago

lagoon-mcl - LAGOON-MCL v1.0.0

First version of LAGOON-MCL (LArge COmparative Omics Network Markov CLustering algorithm). LAGOON-MCL is a pipeline for analyzing omics data. To do this, it builds sequence similarity networks with MCL (Markov Clustering algorithm).

- Python
Published by jroussea about 2 years ago