Nextclade
Nextclade: clade assignment, mutation calling and quality control for viral genomes - Published in JOSS (2021)
Multilocus sequence typing by blast from de novo assemblies against PubMLST
Multilocus sequence typing by blast from de novo assemblies against PubMLST - Published in JOSS (2016)
SaffronTree
SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs. - Published in JOSS (2017)
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
GFF3toEMBL
GFF3toEMBL: Preparing annotated assemblies for submission to EMBL - Published in JOSS (2016)
epialleleR
Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package
genometric.mspc.core
Using combined evidence from replicates to evaluate ChIP-seq peaks
https://github.com/ctriermaansson/dnafusion
Identification of gene-fusions, including EML4-ALK
sammyseq
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
submitdatairidanext
Pipeline for submitting data to INSDC databases for IRIDA Next
ramr
Detection of rare aberrantly methylated regions / epimutations in array and NGS data — an R/Bioc package
fetch_ngs
Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.
