Alternatives and similar repositories for mosdepth

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

• brentp / somalier
  fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"
  ☆283Updated 3 weeks ago
• brentp / slivar
  genetic variant expressions, annotation, and filtering for great good.
  ☆263Updated 3 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆441Updated 3 weeks ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 10 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆422Updated last month
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆594Updated last month
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆470Updated last month
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆254Updated 2 years ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆505Updated 2 months ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆416Updated 5 months ago
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆588Updated 5 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆318Updated 3 years ago
• fulcrumgenomics / fgbio
  Tools for working with genomic and high throughput sequencing data.
  ☆329Updated this week
• TransDecoder / TransDecoder
  TransDecoder source
  ☆291Updated 8 months ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆500Updated last week
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆379Updated last year
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆599Updated 10 months ago
• usadellab / Trimmomatic
  ☆251Updated last year
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆510Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆268Updated last year
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆258Updated 3 months ago
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆482Updated last year
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆299Updated last year
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated 11 months ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆387Updated 5 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆442Updated last year
• jtamames / SqueezeMeta
  A complete pipeline for metagenomic analysis
  ☆416Updated this week
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆409Updated 4 months ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆446Updated this week
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆212Updated last year