Alternatives and similar repositories for flair:

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

• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆210Updated this week
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆217Updated 2 weeks ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆266Updated 2 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆137Updated 3 years ago
• epi2me-labs / wf-human-variation
  ☆118Updated last week
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆147Updated 7 months ago
• nanoporetech / modkit
  A bioinformatics tool for working with modified bases
  ☆185Updated last week
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆226Updated 4 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆215Updated 9 months ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆319Updated 3 weeks ago
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆198Updated 2 weeks ago
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆149Updated 2 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆157Updated 2 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆251Updated last year
• kcleal / gw
  Genome browser and variant annotation
  ☆300Updated last week
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆140Updated 2 years ago
• novoalab / EpiNano
  Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
  ☆114Updated 3 weeks ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆200Updated last month
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆302Updated last week
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆208Updated last year
• ablab / IsoQuant
  Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)
  ☆162Updated this week
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆248Updated last month
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆133Updated 10 years ago
• jtlovell / GENESPACE
  ☆204Updated 2 months ago
• Xinglab / rmats-turbo
  ☆249Updated 4 months ago
• wjwei-handsome / wgatools
  Whole Genome Alignment Tools
  ☆172Updated 2 weeks ago
• epi2me-labs / wf-transcriptomes
  ☆90Updated 3 months ago