BU-ISCIII

plasmidID

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

SARS-Cov2_analysis

Documentation for analyzing SARS-Cov2 samples.

nextflow-scif

This is a demo about how to develop and deploy a pipeline using nextflow, scif, a container (Singularity and Docker) and its posterior deployment.

SARS_Cov2_consensus-nf

Nextflow pipeline to analyze SARS-Cov2 Illumina SISPA and/or amplicons data

WGS-Outbreaker

Pipeline for whole genome sequencing analysis for outbreak detection and characterization of foodborne bacteria

qc_exome_tools

panelLowFreq-nf

This is a nextflow pipeline for variant calling of low frequency variants in panel/WES high-throughput data.

iSkyLIMS_drylab

scif_app_recipes

Install recipes for scif and Singularity/Docker containers

exome_pipeline

Miscellaneous pipelines for genomics computation analysis in a SGE HPC platform.

Fastq2uBam

Scripts for converting FASTQ files into unaligned BAM files, and viceversa, conserving all information in the @SEQ_ID field.

iSkyLIMS_core

iSkyLIMS home website for information and links purposes

miRNAs-nf

Nextflow pipeline to analyze miRNA-seq data.

openebench_gmi

PikaVirus-Archived

Open source software that implements a new method for metagenomics analysis. A new mapping approach is integrated with traditional assembly and blast annotation, all integrated in a web-based user friendly visualization platform for ease interpretation.

rnaseq-nf

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

AnsibleRecipes

Each folder contains ansible playbook and all requiered scripts to deploy some of our machines.

bacterial_qc

builder

a template ready to go to easily build, test, and deploy reproducible SCIF containers!

CentOS7_base_image

Static CentOS7 image with updated development tools. It speeds up the creation of containers based on CentOS7.

django_utils

Custom and useful features for django

iSkyLIMS_clinic

maf_haploid

openrobots-web

opentrons_covid19

Documentation and scripts for implementation of station A, B and C

sanger_script

Script for sanger sequencing files delivery.

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

SARS_Cov2_assembly-nf

Pipeline for analyzing sars-cov2 data using an de-novo assembly approximation

test-datasets

Test data to be used for automated testing with the nf-core pipelines

wgMLST-nf