Pinned Repositories
flowcraft
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:
DEN-IM
Dengue virus genotyping from shotgun and targeted metagenomics - A nextflow pipeline
INNUca
INNUENDO quality control of reads, de novo assembly and contigs quality assessment, and possible contamination search
LMAS
LMAS - Last (Meta)Genomic Assembler Standing
metagenomic-assembler-comparison
An attempt to benchmark metagenomic assembly tools
metagenomic-binning-comparison
An attempt to benchmark taxonomic independent metagenomic binning tools
PhD-Thesis
Shit gets real
roProfile
Generation of pan-genome profile files using Roary output.
hAMRonization
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
SARS-CoV-2-Contextual-Data-Specification
Collection template and associated materials for SARS-CoV-2 metadata
cimendes's Repositories
cimendes/metagenomic-assembler-comparison
An attempt to benchmark metagenomic assembly tools
cimendes/PhD-Thesis
Shit gets real
cimendes/wdl_assembly_wf
A small workflow for the assembly of short-read illumina data
cimendes/docker-builds
:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics
cimendes/blu13_exercise_app
repo to solve exercise notebook of ldssa blu13
cimendes/blu14_exercise_app
cimendes/contextual_data_QC_tags
Standardized attributes for labelling sequence datasets with known quality control issues
cimendes/ESCMID-MGE-2022
cimendes/gambitcore
cimendes/gambittools
A suite of tools for working with GAMBIT
cimendes/hAMRonization_workflow
Harmonization of AMR predictor tool outputs
cimendes/heard_lmas
Script to combine LMAS reports into a singular file
cimendes/HMAS-QC-Pipeline2
an alternative pipeline without using mothur
cimendes/HSM_lupus_metataxonomics
cimendes/HYBRIDLMAS_DEMO
HYBRIDLMAS report demo
cimendes/ldssa_blu13
cimendes/learn-wdl
Educational materials for learning WDL
cimendes/lists-conditionals--assignment-problem
lists-conditionals--assignment-problem - React coursework
cimendes/LMAS_DEMO
Demo report for LMAS report
cimendes/LMAS_DEMO_BMOCK12
cimendes/LONGLMAS_DEMO
Demo report for LONGLMAS
cimendes/miniwdl_tutorial
cimendes/nextflow_cheatsheet
Useful tips to get started with Nextflow
cimendes/proCompare
cimendes/public_health_bioinformatics
Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
cimendes/railway-test
cimendes/ribosomal-wdl
A WDL wrapper around ribosomal_snakemake for Terra.bio
cimendes/theiagen_mock_reports
cimendes/Western-WFD-2024
Resource for the Western Region WFD 2024 Training Event
cimendes/zymos_lmas_report