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"
  ☆287Updated last week
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆450Updated 3 weeks ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆477Updated 2 weeks ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆425Updated 2 months ago
• brentp / slivar
  genetic variant expressions, annotation, and filtering for great good.
  ☆262Updated last week
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆514Updated 4 months ago
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆603Updated last week
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆423Updated 6 months ago
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆515Updated last week
• fulcrumgenomics / fgbio
  Tools for working with genomic and high throughput sequencing data.
  ☆335Updated last week
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆458Updated this week
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆487Updated 2 months ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆602Updated 11 months ago
• biod / sambamba
  Tools for working with SAM/BAM data
  ☆593Updated 6 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆255Updated 2 years ago
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆491Updated last year
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆390Updated last year
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆364Updated this week
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆390Updated 7 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆516Updated last year
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆503Updated 8 months ago
• aidenlab / juicer
  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
  ☆451Updated 7 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆379Updated 2 weeks ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆294Updated 9 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆271Updated last year
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆369Updated last month
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆413Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆367Updated 3 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆342Updated 11 months ago