Alternatives and similar repositories for BamQC:

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

• s-andrews / SeqMonk
  SeqMonk NGS visualisation and analysis tool
  ☆49Updated 2 months ago
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 2 years ago
• rvolden / Mandalorion-Episode-II
  Version II of Mandalorion
  ☆32Updated 6 years ago
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆39Updated 7 years ago
• COMBINE-lab / SalmonTools
  Useful tools for working with Salmon output
  ☆37Updated 4 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• tommyau / bamclipper
  Remove primer sequence from BAM alignments by soft-clipping
  ☆31Updated 5 years ago
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆65Updated 2 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated last year
• ljdursi / mergevcf
  Python package and routines for merging VCF files
  ☆29Updated 3 years ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆30Updated last year
• nspies / svviz2
  for visual evaluation of read support for structural variation
  ☆52Updated 9 months ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 8 years ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆48Updated 4 years ago
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆51Updated 5 years ago
• EI-CoreBioinformatics / portcullis
  Splice junction analysis and filtering from BAM files
  ☆39Updated 2 years ago
• mskilab-org / gGnome
  R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
  ☆39Updated this week
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆45Updated this week
• imbforge / NGSpipe2go
  a set of NGS pipelines
  ☆24Updated this week
• stephenturner / adapters
  Adapters for trimming
  ☆30Updated 6 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 2 years ago
• namphuon / ViFi
  Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
  ☆27Updated 3 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆95Updated 11 months ago
• TheJacksonLaboratory / SVE
  ☆51Updated 5 years ago
• scottgigante / haplotyped-methylome
  Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
  ☆23Updated 6 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆56Updated 3 years ago
• xuchang116 / smCounter
  smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…
  ☆20Updated 5 years ago
• stephenfloor / extract-transcript-regions
  For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…
  ☆35Updated last year
• SdeBlank / NanoFG
  Third-generation fusion gene detection
  ☆14Updated last year