Alternatives and similar repositories for doc-ANNOVAR:

Users that are interested in doc-ANNOVAR are comparing it to the libraries listed below

• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆250Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆235Updated last week
• pcingola / SnpEff
  ☆264Updated last month
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆264Updated last year
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆221Updated 4 years ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆460Updated 3 weeks ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆221Updated last week
• WGLab / InterVar
  A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
  ☆191Updated last year
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆267Updated last month
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆288Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆540Updated 8 months ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆355Updated 3 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆314Updated 3 years ago
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆145Updated 6 months ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆183Updated this week
• TransDecoder / TransDecoder
  TransDecoder source
  ☆285Updated 5 months ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆194Updated last year
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆131Updated 10 years ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆366Updated 3 years ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆160Updated last week
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆207Updated last week
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆264Updated last year
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆295Updated 3 years ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆210Updated last week
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆354Updated 2 years ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆197Updated last week
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆246Updated last week
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆208Updated 3 weeks ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago