Alternatives and similar repositories for sarek

Users that are interested in sarek are comparing it to the libraries listed below

• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆513Updated 4 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆425Updated 2 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆449Updated 2 weeks ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆422Updated 6 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆342Updated 11 months ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆515Updated this week
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆511Updated this week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆444Updated last year
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆216Updated last week
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆490Updated last year
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆495Updated this week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆254Updated 2 years ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆399Updated 3 weeks ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆298Updated 2 years ago
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆412Updated last year
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆434Updated 2 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆244Updated 3 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆271Updated last year
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆369Updated 3 weeks ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆389Updated 7 months ago
• usadellab / Trimmomatic
  ☆256Updated last year
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆450Updated 7 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆475Updated 2 weeks ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆723Updated last week
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆335Updated 3 weeks ago
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆580Updated 11 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆748Updated 3 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆633Updated 3 weeks ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆826Updated last year