Alternatives and similar repositories for kentUtils:

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

• AstraZeneca-NGS / VarDict
  VarDict
  ☆195Updated last year
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆157Updated 2 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆249Updated last year
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆319Updated last year
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆212Updated 10 months ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆315Updated 3 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆214Updated 8 months ago
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆169Updated 9 months ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆140Updated 2 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆244Updated 2 weeks ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆240Updated 2 years ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆133Updated 10 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆196Updated 3 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆235Updated this week
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆124Updated 4 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆267Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆539Updated 8 months ago
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆194Updated last month
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆247Updated 3 weeks ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆371Updated last year
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆159Updated 7 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆213Updated this week
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆185Updated this week
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆246Updated 2 weeks ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆267Updated last month
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆264Updated last year
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆297Updated 11 months ago