Alternatives and similar repositories for cDNA_Cupcake:

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

• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆200Updated 3 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆203Updated this week
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆536Updated 6 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆245Updated last year
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆238Updated 3 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆206Updated last year
• TransDecoder / TransDecoder
  TransDecoder source
  ☆283Updated 3 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆259Updated 7 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆215Updated 3 years ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆138Updated last year
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆106Updated last year
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆216Updated this week
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆240Updated 2 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆231Updated 2 months ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆133Updated 3 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆209Updated 6 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆310Updated 3 years ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆345Updated 2 years ago
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆286Updated last year
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆130Updated 9 years ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆230Updated last year
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆207Updated last year
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆200Updated 2 months ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆209Updated 3 weeks ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆355Updated last month
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆273Updated 3 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆155Updated last year
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆268Updated 7 months ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆251Updated 3 weeks ago
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆216Updated last year