Alternatives and similar repositories for pysamstats:

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

• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆157Updated 2 years ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆130Updated 4 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆215Updated 9 months ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆142Updated last month
• epi2me-labs / wf-transcriptomes
  ☆90Updated 3 months ago
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆148Updated 10 months ago
• biocorecrg / master_of_pores
  Nextflow pipeline for analysis of direct RNA Nanopore reads
  ☆101Updated this week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆197Updated last year
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆151Updated 2 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆266Updated 2 months ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆149Updated 2 years ago
• parklab / bamsnap
  ☆119Updated 5 months ago
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆147Updated this week
• epi2me-labs / wf-human-variation
  ☆118Updated last week
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆148Updated 7 months ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆81Updated 2 years ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆191Updated last month
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆137Updated 3 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆210Updated this week
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆244Updated last month
• MariaNattestad / Assemblytics
  Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference gen…
  ☆140Updated 5 months ago
• brentp / jigv
  igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
  ☆126Updated last year
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆173Updated 3 years ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• yfukasawa / LongQC
  LongQC is a tool for the data quality control of the PacBio and ONT long reads.
  ☆160Updated last year
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆184Updated 10 months ago
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆116Updated 6 years ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆209Updated 3 months ago