Alternatives and similar repositories for training:

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

• nf-core / fetchngs
  Pipeline to fetch metadata and raw FastQ files from public databases
  ☆164Updated 3 weeks ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆134Updated 3 years ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆302Updated 3 months ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆206Updated this week
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆191Updated 3 weeks ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆218Updated 4 years ago
• GoekeLab / bambu
  Reference-guided transcript discovery and quantification for long read RNA-Seq data
  ☆197Updated this week
• rajewsky-lab / mirdeep2
  Discovering known and novel miRNAs from small RNA sequencing data
  ☆142Updated 5 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆202Updated 3 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆260Updated 2 weeks ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆207Updated last year
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆217Updated last week
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆157Updated 2 weeks ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆209Updated last month
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆140Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆261Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆247Updated last year
• nf-core / mag
  Assembly and binning of metagenomes
  ☆228Updated this week
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆130Updated 9 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆295Updated this week
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆204Updated last week
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆240Updated 2 weeks ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆107Updated 2 years ago
• nf-core / differentialabundance
  Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
  ☆72Updated this week
• nf-core / taxprofiler
  Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
  ☆136Updated this week
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆232Updated 3 months ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆320Updated 3 months ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆211Updated 7 months ago
• nf-core / viralrecon
  Assembly and intrahost/low-frequency variant calling for viral samples
  ☆131Updated 3 weeks ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆252Updated last month