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
  ☆161Updated 2 years ago
• parklab / bamsnap
  ☆123Updated last week
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆151Updated last year
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆237Updated 3 weeks ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆247Updated last month
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆191Updated this week
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆149Updated 3 weeks ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆116Updated 7 years ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆141Updated 2 years ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆134Updated 2 years ago
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆143Updated 8 years ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆244Updated 9 months ago
• OpenGene / fastv
  An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infect…
  ☆118Updated last year
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆154Updated 3 years ago
• MikkelSchubert / adapterremoval
  AdapterRemoval v2 - rapid adapter trimming, identification, and read merging
  ☆113Updated 2 months ago
• GregoryFaust / samblaster
  samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
  ☆234Updated 3 years ago
• epi2me-labs / wf-human-variation
  ☆131Updated last week
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆155Updated 5 months ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 6 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆164Updated 11 months ago
• brentp / bwa-meth
  fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
  ☆150Updated last week
• ExpressionAnalysis / ea-utils
  Automatically exported from code.google.com/p/ea-utils
  ☆96Updated 2 years ago
• ComparativeGenomicsToolkit / hal
  Hierarchical Alignment Format
  ☆170Updated 7 months ago
• mdshw5 / fastqp
  Simple FASTQ quality assessment using Python
  ☆109Updated 4 years ago
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆159Updated last week
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆134Updated 4 years ago
• lh3 / readfq
  Fast multi-line FASTA/Q reader in several programming languages
  ☆176Updated 4 years ago