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
  ☆156Updated last year
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆157Updated 5 months ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆211Updated 7 months ago
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆147Updated 5 months ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆127Updated 3 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆192Updated last year
• simon-anders / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆123Updated 4 years ago
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆169Updated 8 months ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆132Updated 2 years ago
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆144Updated 8 months ago
• parklab / bamsnap
  ☆119Updated 3 months ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆107Updated 2 years ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆179Updated this week
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• epi2me-labs / wf-transcriptomes
  ☆86Updated last month
• biocorecrg / master_of_pores
  Nextflow pipeline for analysis of direct RNA Nanopore reads
  ☆101Updated 2 months ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆237Updated 4 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆237Updated last month
• GoekeLab / sg-nex-data
  Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
  ☆115Updated last month
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆141Updated last year
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆146Updated this week
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆183Updated 9 months ago
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆140Updated last month
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• ComparativeGenomicsToolkit / hal
  Hierarchical Alignment Format
  ☆166Updated last month
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆81Updated 2 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆202Updated 3 months ago
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆181Updated 2 months ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆245Updated 8 months ago
• epi2me-labs / wf-human-variation
  ☆110Updated 2 weeks ago