Alternatives and similar repositories for needlestack

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

• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 9 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated 2 years ago
• Ettwiller / Damage-estimator
  Estimate damage in standard NGS library preparation. Incompatible with library preparation methods from which the imbalance is lost (such…
  ☆54Updated 8 years ago
• s-andrews / BamQC
  Mapped QC analysis program
  ☆44Updated 7 years ago
• ikalatskaya / ISOWN
  ☆46Updated 6 years ago
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 3 years ago
• lh3 / CHM-eval
  ☆55Updated 5 years ago
• Oshlack / STRetch
  Method for detecting STR expansions from short-read sequencing data
  ☆63Updated 4 years ago
• pmelsted / pizzly
  Fast fusion detection using kallisto
  ☆79Updated 7 months ago
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 8 years ago
• quinlan-lab / vcf2db
  create a gemini-compatible database from a VCF
  ☆55Updated 5 years ago
• tommyau / bamclipper
  Remove primer sequence from BAM alignments by soft-clipping
  ☆31Updated 6 years ago
• statgen / gotcloud
  Genomes on the Cloud, Mapping & Variant Calling Pipelines
  ☆33Updated 8 years ago
• mskcc / mutation-signatures
  Create mutation signatures from MAF's, and decompose them into Stratton signatures
  ☆60Updated 6 years ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 6 years ago
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆42Updated 4 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆79Updated 2 years ago
• sfu-compbio / sinvict
  SiNVICT: Ultra-Sensitive Detection of Single Nucleotide Variants and Indels in Circulating Tumour DNA
  ☆27Updated 5 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆59Updated last year
• biocore-ntnu / epic
  (DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
  ☆31Updated 7 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆74Updated 6 years ago
• getzlab / deTiN
  DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…
  ☆53Updated 3 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆40Updated 4 years ago
• sigven / gvanno
  Generic human DNA variant annotation pipeline
  ☆59Updated last year
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated 2 years ago
• taylor-lab / hotspots
  Identifying recurrent mutations in cancer
  ☆39Updated 4 years ago