Alternatives and similar repositories for hisat-genotype

Users that are interested in hisat-genotype are comparing it to the libraries listed below

• deepomicslab / SpecHLA
  SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …
  ☆46Updated 3 months ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆53Updated 3 weeks ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 6 years ago
• ferrannadeu / IgCaller
  Python program designed to reconstruct immunoglobulin gene rearrangements and oncogenic translocations from WGS, WES and capture NGS in l…
  ☆20Updated last year
• SyntekabioTools / HLAscan
  ☆25Updated 5 years ago
• mhalushka / miRge3.0
  Comprehensive analysis of small RNA sequencing data
  ☆31Updated last month
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 2 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 11 months ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 7 years ago
• EI-CoreBioinformatics / portcullis
  Splice junction analysis and filtering from BAM files
  ☆40Updated 3 years ago
• pughlab / ConsensusCruncher
  ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…
  ☆21Updated 2 years ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆43Updated 7 years ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆31Updated 2 years ago
• nf-core / lncpipe
  UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
  ☆34Updated 2 months ago
• zavolanlab / zarp
  The Zavolab Automated RNA-seq Pipeline
  ☆35Updated last month
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆42Updated last week
• hbctraining / Intro-to-rnaseq-hpc-salmon
  ☆49Updated 4 years ago
• brwnj / fastq-multx
  Demultiplexes a fastq.
  ☆45Updated 4 years ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• 4ureliek / TEanalysis
  Analysis of TE contribution to features (transcripts or simple features). Includes utils to test enrichment.
  ☆27Updated 5 years ago
• hidelab / diffcoexp
  Differential coexpression analysis
  ☆15Updated last year
• pinellolab / AmpUMI
  Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
  ☆41Updated last year
• nloyfer / UXM_deconv
  ☆43Updated 2 years ago
• NBISweden / GUESSmyLT
  An efficient way to guess the library type of your RNA-Seq data.
  ☆31Updated 2 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 2 years ago
• lindaszabo / KNIFE
  Known and Novel IsoForm Explorer. Statistically based splicing detection for circular and linear isoforms
  ☆32Updated 7 years ago
• nanoporetech / pipeline-pinfish-analysis
  Pipeline for annotating genomes using long read transcriptomics data with pinfish
  ☆28Updated 4 years ago