Software

From Bioinformatics Core Wiki
Revision as of 12:30, 26 February 2020 by Thermoso (Talk | contribs)


VectorQC: NextFlow pipeline for assembly and annotation of DNA vectors (https://github.com/biocorecrg/vectorQC)
Transcriptome assembly: Nextflow pipeline for de novo transcriptome assembly and annotation based on Trinity and Transdecoder (https://github.com/biocorecrg/transcriptome_assembly)
TEQC: R package for Quality control of target capture experiments (https://www.bioconductor.org/packages/devel/bioc/html/TEQC.html)
Mothur procedures: Shell scripts for processing ITS (fungi) and 16S rRNA (bacteria) amplicon sequencing data (MiSeq) in mothur. (https://github.com/biocorecrg/microbiome_procedures)
Master of Pores: Nextflow pipeline for analysis of direct RNA Nanopore reads (https://github.com/biocorecrg/master_of_pores)
Indrop-Flow: Indrops analysis pipeline based on DropEST (https://github.com/biocorecrg/indrop)
HiC-inspector: High-throughput conformation capture (Hi-C) allows to study the three-dimensional architecture of whole genomes through the detection of long range chromosomal interactions (https://github.com/HiC-inspector/HiC-inspector)
FA-nf (functional annotation): NextFlow pipeline for functional annotation of proteins from non-model organisms based on InterPro and Blast (https://github.com/guigolab/FA-nf)
Bioinformatics Core Facility @ CRG — 2011-2020