Rename and documentation service catalog

[saramonzon]

Services renamed in iskylims.isciiides.es, need docs!!

[svarona]

• [x] Viralrecon:
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (.txt & .xlsx)
    • samples_ref xlsx
    • amplicon primers .bed file for mapping
    • amplicon primers .fasta file por assembly
  • [x] Bioinformatic analysis steps
• [x] IRMA
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (no needed)
  • [x] Bioinformatic analysis steps
• [x] PikaVirus:
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (no needed)
  • [x] Bioinformatic analysis steps
• [x] assembly:
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (no needed)
  • [x] Bioinformatic analysis steps
• [x] mRNAseq:
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (.txt & .xlsx)
    • clin_data
    • Comparatived
  • [x] Bioinformatic analysis steps
• [ ] miRNAseq:
  • [ ] Analysis procedure markdown
  • [ ] Results folder markdown
  • [ ] Input needed documentation (.txt & .xlsx)
    • clin_data
    • Adapters
    • Comparatives
  • [ ] Bioinformatic analysis steps
• [x] MAG:
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (no needed)
  • [x] Bioinformatic analysis steps
• [x] Trios:
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (only .txt with explanations)
    • .bed file
    • pedigry
  • [x] Bioinformatic analysis steps
• [x] ExomeEB:
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (only .txt with explanations)
    • Gene list (only when they change)
    • .bed file
    • pedigry
  • [x] Bioinformatic analysis steps
• [x] WGS-TRIO:
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (only .txt with explanations)
    • pedigry
  • [x] Bioinformatic analysis steps
• [ ] RBpanel:
  • [ ] Analysis procedure markdown
  • [ ] Results folder markdown
  • [ ] Input needed documentation (only .txt with explanations)
    • .bed file
  • [ ] Bioinformatic analysis steps
• [x] wg/cgMLST:
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (only .txt with explanations)
    • Schema
  • [x] Bioinformatic analysis steps
• [ ] Resistencias y virulencias:
  • [ ] Analysis procedure markdown
  • [ ] Results folder markdown
  • [x] Input needed documentation (no needed)
  • [ ] Bioinformatic analysis steps
• [x] Plásmidos:
  • [x] Analysis procedure markdown
  • [x] Results folder markdown
  • [x] Input needed documentation (only .txt with explanations)
    • Databases
  • [x] Bioinformatic analysis steps
• [ ] 16s metagenomica:
  • [ ] Analysis procedure markdown
  • [ ] Results folder markdown
  • [ ] Input needed documentation (only .txt with explanations)
    • Databases
    • Adapters
  • [ ] Bioinformatic analysis stepsn

[svarona]

Service catalog: Genomic Data Analysis:

• [x] Pre-processing and quality analysis
  • [x] Sequence quality analysis and host genome removal (seek_and_destroy)
• [x] Next Generation Sequencing data analysis
  • [x] DNAseq / cDNAseq: Exome sequencing (WES) / Genome sequencing (WGS) / Targeted sequencing
    • [x] Low-frequency variants detection and annotation for whole genome or sequencing panel (e.g. retinoblastoma gene panel) (lowfreq_panel)
    • [x] Eukaria: Variant calling and annotation for a sequencing panel (e.g. epidermolysis gene panel, mouse or rat gene panel) (exomeeb)
    • [X] Eukaria (non-human): Variant calling, annotation and SNP-based outbreak analysis (e.g. diploid fungal outbreak) (TODO freebayes_outbreak)
    • [x] Human: Exome sequencing for variant calling, annotation and inheritance filtering (e.g. Exome sequencing of a human trio (two parents and one child)) (exometrio)
    • [x] Human: Whole genome sequencing for SNPs variant calling, annotation and inheritance filtering (e.g.WGS of a human trio ) (wgstrio)
    • [x] Fungal / bacteria / virus : Variant calling, annotation and SNP-based outbreak analysis (e.g. haploid fungal outbreak) (snippy)
    • [x] Bacteria: De novo genome assembly and annotation (Assembly)
    • [x] Bacteria: In-depth analysis of Mycobacterium species genomes (e.g. M. tuberculosis. M. bovis) (MTBSeq)
    • [x] Bacteria: Plasmid analysis and characterization (PlasmidID)
    • [x] Bacteria: Multi-Locus Sequence Typing (MLST), analysis of virulence factors, antimicrobial resistance, and plasmids characterization (characterization)
    • [x] Bacteria: Core genome or whole genome Multi-Locus Sequence Typing analysis (cg/wgMLST) (wgmlst_chewbbaca)
    • [x] Viral: Genomic reconstruction, variant calling and de novo assembly (viralrecon)
    • [x] Viral Flu: Influenza fragment reconstruction and variant detection (IRMA)
  • [X] RNAseq: Transcriptome sequencing (rnaseq)
    • [x] Differential Gene Expression (DEG) (rnaseq)
    • [x] Differential transcript expression (DET) (rnaseq)
    • [X] Differential miRNA expression (DEM) (TODO mirnaseq)
    • [X] Gene expression changes over a series of time points (TODO timeseries_rnaseq)
  • [X] Metagenomics and targeted metagenomics
    • [X] Taxonomic based Identification and classification of organisms in complex communities (mag_met)
    • [X] De novo assembly contigs' alignment to database (blast_nt)
    • [X] Bacteria: 16S rRNA gene analysis to assess bacterial diversity (TODO 16s_metagenomics)
    • [x] Viral: Detection and characterization of viral genomes within metagenomic data (pikavirus)

[svarona]

• Viralrecon
  • [ ] Documentación
  • [ ] Netflow: Mejoras:
    • [ ] MultiQC con > 2000 muestras
    • [x] GTF custom de SARS
    • [x] Nanopore custom bed
    • [ ] Testar bien el iVar variants to vcf
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
• PikaVirus
  • [x] Documentación
  • [x] Netflow
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
• IRMA
  • [x] Documentación
  • [ ] Netflow
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
• Assembly
  • [x] Documentación
  • [x] Netflow
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
  • mRNAseq:
  • [x] Documentación
  • [x] Netflow
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
• miRNAseq:
  • [ ] Documentación
  • [x] Netflow
  • [ ] Template bu-isciii-tools
  • [ ] Data set de validación
• MAG:
  • [x] Documentación
  • [x] Netflow
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
• Trios:
  • [ ] Documentación
  • [x] Netflow
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
• RBpane:
  • [ ] Documentación
  • [ ] Netflow
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
• wg/cgMLST:
  • [x] Documentación
  • [ ] Netflow
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
• Resistencias y virulencias:
  • [ ] Documentación
  • [ ] Netflow
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
• Plásmidos:
  • [x] Documentación
  • [ ] Netflow
  • [x] Template bu-isciii-tools
  • [ ] Data set de validación
• 16s metagenomica:
  • [ ] Documentación
  • [ ] Netflow
  • [ ] Template bu-isciii-tools @svarona
  • [ ] Data set de validación