Alternatives and similar repositories for hts-python

Users that are interested in hts-python are comparing it to the libraries listed below

• brentp / geneimpacts
  prioritize effects of variant annotations from VEP, SnpEff, et al.
  ☆34Updated last year
• brentp / gsort
  sort genomic data
  ☆36Updated 3 months ago
• rhshah / iCallSV
  A Framework to call Structural Variants from NGS based datasets
  ☆22Updated 8 years ago
• ryanlayer / svv
  Stupid Simple Structural Variant View
  ☆25Updated 9 years ago
• TheJacksonLaboratory / pyBedGraph
  A Python package for fast operations on 1-dimensional genomic signal tracks
  ☆23Updated 5 years ago
• cdarby / samovar
  Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters
  ☆23Updated 6 years ago
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated 2 years ago
• mtw / Bio-ViennaNGS
  A Perl extension and collection of utilities for Next-Generation Sequencing (NGS) data analysis
  ☆23Updated 3 months ago
• jeremymcrae / clinical-filter
  filtering trio-based genetic variants in VCFs for clinical review
  ☆21Updated 5 years ago
• langmead-lab / reference_flow
  Reducing reference bias using multiple population reference genomes
  ☆34Updated last year
• aganezov / RCK
  RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes
  ☆18Updated 5 years ago
• ccgd-profile / BreaKmer
  A method to identify structural variation from sequencing data in target regions
  ☆32Updated 5 years ago
• ssadedin / ximmer
  Ximmer is a system for CNV calling on exome and targeted genomic sequencing
  ☆19Updated last week
• quinlan-lab / pathoscore
  pathoscore evaluates variant pathogenicity tools and scores.
  ☆22Updated 3 years ago
• BenLangmead / qtip
  Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities
  ☆25Updated 6 years ago
• vpc-ccg / calib
  Calib clusters barcode tagged paired-end reads based on their barcode and sequence similarity.
  ☆40Updated 2 years ago
• Magdoll / CoSA
  Coronavirus (SARS-Cov-2) sequencing analysis
  ☆10Updated 4 years ago
• brentp / hts-python
  pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)
  ☆49Updated 8 years ago
• bcgsc / SSAKE
  🍶 Genome assembly with short sequence reads
  ☆25Updated 2 years ago
• jts / bri
  Bam Read Index - Extract alignments from a bam file by readname
  ☆28Updated last year
• cschin / Write_A_Genome_Assembler_With_IPython
  The repository keeps the files for an IPython notebook on about how to make a simple genome assembler using python
  ☆30Updated 7 years ago
• J35P312 / FindSV
  Structural variant pipeline
  ☆18Updated 5 years ago
• brentp / cigar
  simple library for dealing with SAM cigar strings
  ☆41Updated 4 years ago
• lh3 / pre-pe
  Preprocessing paired-end reads produced with experiment-specific protocols
  ☆32Updated 7 years ago
• quinlan-lab / vcf2db
  create a gemini-compatible database from a VCF
  ☆55Updated 5 years ago
• YingZhou001 / Immuannot
  Immuological gene typing and annotation for genome assembly
  ☆38Updated 10 months ago
• mcfrith / dnarrange
  ☆16Updated last year
• nanoporetech / minimappy
  Python bindings to minimap2
  ☆16Updated 8 years ago
• ding-lab / BreakPointSurveyor
  A comprehensive pipeline to analyze and visualize structural variants
  ☆20Updated 6 years ago
• grocsvs / grocsvs
  Genome-wide reconstruction of complex structural variants
  ☆39Updated 3 years ago