Alternatives and similar repositories for sambamba

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

• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆492Updated 2 weeks ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆434Updated 3 months ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆852Updated 5 months ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆450Updated last year
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆455Updated last year
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆531Updated 2 months ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆428Updated 6 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆555Updated last year
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆471Updated last week
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆513Updated last month
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆624Updated last week
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆795Updated last month
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆519Updated 2 months ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆387Updated 3 years ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆1,007Updated 8 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆742Updated 3 months ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆402Updated 3 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆328Updated 5 months ago
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆415Updated last month
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆446Updated 10 months ago
• vcflib / vcflib
  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
  ☆660Updated 3 weeks ago
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆467Updated 2 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆389Updated 2 months ago
• gmarcais / Jellyfish
  A fast multi-threaded k-mer counter
  ☆519Updated last year
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆502Updated this week
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆510Updated last week
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆846Updated 2 weeks ago
• usadellab / Trimmomatic
  ☆274Updated last month
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆541Updated 2 months ago