Alternatives and similar repositories for IndexTools

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

• DecodeGenetics / read_haps
  Detects human contamination in bam files
  ☆16Updated 5 years ago
• SeqOne / variant_alert
  Variant Alert!, a framework to monitor every significant alteration in variant classification and gene-disease association between two ve…
  ☆14Updated 4 years ago
• jaudoux / kamix
  Index and query k-mer matrices in BGZF
  ☆12Updated 7 years ago
• SeqOne / clinvcf
  Generate an enhanced VCF files from ClinVar XML Full releases
  ☆15Updated 2 years ago
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated 11 months ago
• ssadedin / ximmer
  Ximmer is a system for CNV calling on exome and targeted genomic sequencing
  ☆19Updated 2 weeks ago
• edawson / svaha2
  Linear-time, low-memory construction of variation graphs
  ☆20Updated 5 years ago
• jts / bri
  Bam Read Index - Extract alignments from a bam file by readname
  ☆27Updated last year
• jbelyeu / unfazed
  Unfazed by genomic variant phasing
  ☆27Updated last year
• mskilab-org / pgv
  Pan gGnome Viewer
  ☆10Updated 2 months ago
• DecodeGenetics / popvcf
  Lossless VCF compression
  ☆20Updated 3 years ago
• namsyvo / IVC
  Integrated Variant Caller
  ☆17Updated 7 years ago
• J35P312 / FindSV
  Structural variant pipeline
  ☆17Updated 5 years ago
• medvedevgroup / vargeno
  Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
  ☆21Updated 6 years ago
• mreppell / Karp
  Accurate and fast taxonomic classification using pseudoaligning
  ☆21Updated 8 years ago
• nh13 / fqme
  ☆21Updated 10 months ago
• fulcrumgenomics / fgsv
  Tools to gather evidence for structural variation via breakpoint detection.
  ☆19Updated 5 months ago
• aganezov / RCK
  RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes
  ☆17Updated 5 years ago
• nygenome / Lancet2
  v2.x of the microassembly based somatic variant caller
  ☆23Updated 2 months ago
• myriad-opensource / samwell
  Samwell: a python package for using genomic files... well
  ☆20Updated 3 years ago
• cdarby / samovar
  Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters
  ☆23Updated 6 years ago
• brentp / tnsv
  add true-negative SVs from a population callset to a truth-set.
  ☆15Updated 3 years ago
• BenLangmead / qtip
  Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities
  ☆25Updated 5 years ago
• brentp / seqcover
  seqcover allows users to view coverage for hundreds of genes and dozens of samples
  ☆52Updated 4 years ago
• langmead-lab / reference_flow
  Reducing reference bias using multiple population reference genomes
  ☆33Updated last year
• biodata-fun / htslib_howto
  Collection of simple C scripts for parsing vcf or bam files using the htslib C library. These scripts can be used as the starting point f…
  ☆11Updated 4 years ago
• HurlesGroupSanger / indelible
  Structural Variation breakpoint discovery via adaptive learning
  ☆16Updated 2 years ago
• lh3 / klib.nim
  Experimental getopt, gzip reader, FASTA/Q parser and interval queries in nim-lang
  ☆31Updated 5 years ago
• mchaisso / mcutils
  ☆12Updated 3 weeks ago
• sigven / cacao
  Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
  ☆21Updated 4 years ago