Alternatives and similar repositories for bam-readcount:

Users that are interested in bam-readcount are comparing it to the libraries listed below

• pcingola / SnpEff
  ☆261Updated last month
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆262Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆245Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆259Updated last year
• AstraZeneca-NGS / VarDict
  VarDict
  ☆191Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆535Updated 6 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆228Updated this week
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆237Updated 2 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆307Updated 11 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆200Updated 2 months ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆195Updated 3 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆230Updated 2 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆154Updated 3 weeks ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆306Updated last year
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆366Updated last year
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆256Updated 6 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆306Updated 7 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆155Updated last year
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆237Updated 2 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆200Updated this week
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆286Updated last year
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆367Updated last year
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆213Updated 2 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆215Updated 3 years ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆217Updated this week
• TransDecoder / TransDecoder
  TransDecoder source
  ☆281Updated 3 months ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆237Updated last month
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆208Updated 4 years ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆133Updated 3 years ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆236Updated 2 months ago