Alternatives and similar repositories for kent

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

• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆241Updated 2 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆545Updated last year
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆145Updated 10 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆351Updated 4 months ago
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆306Updated last year
• ENCODE-DCC / kentUtils
  UCSC command line bioinformatic utilities
  ☆185Updated last year
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆383Updated 2 weeks ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆259Updated 2 years ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆298Updated 2 years ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆275Updated last year
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆262Updated last week
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆246Updated 3 weeks ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆237Updated last week
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆244Updated last month
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆434Updated 8 months ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆381Updated 3 years ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆176Updated 2 weeks ago
• pcingola / SnpEff
  ☆290Updated 2 weeks ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆318Updated last week
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆234Updated this week
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆376Updated 3 months ago
• kcleal / gw
  Genome browser and variant annotation
  ☆376Updated last month
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆272Updated this week
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆157Updated 3 weeks ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆280Updated last year
• The-Sequence-Ontology / Specifications
  GFF and GVF specification documents
  ☆214Updated last year