Alternatives and similar repositories for lollipops:

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

• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆314Updated last year
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆245Updated 8 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆237Updated last month
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆132Updated 2 years ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆369Updated last year
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆211Updated 7 months ago
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆169Updated 8 months ago
• ryanlayer / giggle
  Interval data structure
  ☆231Updated 2 months ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆195Updated 3 years ago
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆139Updated this week
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆269Updated 8 months ago
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆187Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆538Updated 7 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆247Updated last year
• brentp / goleft
  goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary
  ☆219Updated 4 months ago
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆293Updated 10 months ago
• vibansal / HapCUT2
  software tools for haplotype assembly from sequence data
  ☆215Updated last week
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆312Updated 3 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆157Updated 6 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆203Updated 3 months ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆192Updated last year
• g2nb / igv-jupyter
  Extension for Jupyter which integrates igv.js
  ☆154Updated 2 years ago
• pcingola / SnpEff
  ☆263Updated last week
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆266Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆261Updated last year
• sequana / sequana
  Sequana: a set of Snakemake NGS pipelines
  ☆145Updated last week
• 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
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆206Updated this week
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆144Updated 8 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆204Updated last week