Alternatives and similar repositories for AfterQC:

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

• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆155Updated 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
  ☆261Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆310Updated 3 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆209Updated 6 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆259Updated 7 months ago
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆319Updated 2 years ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 2 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆536Updated 6 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆200Updated 3 months ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆192Updated last year
• TransDecoder / TransDecoder
  TransDecoder source
  ☆283Updated 3 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆263Updated last year
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆213Updated 2 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆231Updated 2 months ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆241Updated 7 months ago
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆119Updated 2 years ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆238Updated 3 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆215Updated 3 years ago
• OpenGene / MutScan
  Detect and visualize target mutations by scanning FastQ files directly
  ☆149Updated 2 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆240Updated 2 months ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆130Updated 9 years ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆306Updated last year
• ENCODE-DCC / rna-seq-pipeline
  ☆146Updated 2 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆308Updated last year
• pcingola / SnpEff
  ☆261Updated 2 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆231Updated 2 weeks ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆155Updated 5 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆402Updated 3 weeks ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆196Updated this week