Alternatives and similar repositories for nf-repeatmasking

Users that are interested in nf-repeatmasking are comparing it to the libraries listed below

• IARCbioinfo / alignment-nf
  Whole Exome/Whole Genome Sequencing alignment pipeline
  ☆28Updated 10 months ago
• EI-CoreBioinformatics / portcullis
  Splice junction analysis and filtering from BAM files
  ☆40Updated 3 years ago
• lconde-ucl / DGE
  Nextflow pipeline that runs DESeq2 on data processed with the nextflow RNAseq pipeline
  ☆12Updated last year
• Gabaldonlab / jloh
  A tool to extract LOH blocks from VCF, BAM and FASTA data
  ☆23Updated 11 months ago
• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated 5 months ago
• myriad-opensource / samwell
  Samwell: a python package for using genomic files... well
  ☆20Updated 3 years ago
• telatin / covtobed
  ⛰ covtobed | Convert the coverage track from a BAM file into a BED file
  ☆45Updated last month
• gzhmat / ShinyCNV
  a Shiny/R application to view and annotate copy number variations
  ☆28Updated 2 years ago
• mgaleyuw / MeOW
  Automated Detection and Qualification of Differential Methylation
  ☆14Updated last year
• lh3 / pre-pe
  Preprocessing paired-end reads produced with experiment-specific protocols
  ☆32Updated 7 years ago
• brentp / fraguracy
  overlapping bases in read-pairs from a fragment indicate accuracy and reveal error-prone sites
  ☆33Updated 2 months ago
• mskilab-org / gGnome
  R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
  ☆41Updated last week
• alevar / tiebrush
  Summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)
  ☆17Updated last week
• rdemolgen / SavvySuite
  Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes
  ☆30Updated last week
• hsinnan75 / MapCaller
  MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
  ☆30Updated 4 years ago
• nf-core / deepvariant
  Please consider using/contributing to https://github.com/nf-core/sarek
  ☆40Updated 4 years ago
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆57Updated 3 years ago
• langmead-lab / reference_flow
  Reducing reference bias using multiple population reference genomes
  ☆32Updated last year
• jbelyeu / unfazed
  Unfazed by genomic variant phasing
  ☆27Updated last year
• PacificBiosciences / svpack
  Structural variant (SV) analysis tools
  ☆36Updated last year
• biocorecrg / MOP2
  Master of Pores 2
  ☆23Updated 8 months ago
• vicsanga / Postre
  POSTRE: Prediction Of STRuctural variant Effects
  ☆27Updated 5 months ago
• fmalmeida / ngs-preprocess
  A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
  ☆34Updated last year
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆26Updated 7 years ago
• lh3 / unicall
  A wrapper for calling small variants from human germline high-coverage single-sample Illumina data
  ☆14Updated 6 years ago
• AstraZeneca-NGS / simple_sv_annotation
  Simplify snpEff annotations for interesting cases
  ☆22Updated 6 years ago
• wassermanlab / Variant_catalogue_pipeline
  Variant catalogue pipeline
  ☆25Updated 3 months ago
• COMBINE-lab / SalmonTools
  Useful tools for working with Salmon output
  ☆38Updated 5 years ago
• robsyme / nextflow-annotate
  Workflows I find helpful for fungal genome annotation
  ☆21Updated 2 years ago
• sigven / cacao
  Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
  ☆21Updated 4 years ago