Alternatives and similar repositories for ShortStack

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

• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆91Updated 3 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆90Updated 2 months ago
• hzi-bifo / RiboDetector
  Accurate and rapid RiboRNA sequences Detector based on deep learning
  ☆115Updated last year
• gencorefacility / variant-calling-pipeline-gatk4
  Variant Calling Pipeline Using GATK4 and Nextflow
  ☆58Updated 2 years ago
• Trinotate / Trinotate
  Trinotate source code
  ☆83Updated last year
• PacificBiosciences / barcoding
  Lima - Demultiplex Barcoded PacBio Samples
  ☆67Updated 4 months ago
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆152Updated last year
• Dfam-consortium / TETools
  Dfam Transposable Element Tools Docker container.
  ☆100Updated 3 weeks ago
• NAL-i5K / GFF3toolkit
  Python programs for processing GFF3 files
  ☆100Updated last year
• PacificBiosciences / pb-assembly
  PacBio Assembly Tool Suite: Reads in ⇨ Assembly out
  ☆118Updated 5 years ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆74Updated 3 years ago
• Trinotate / Trinotate.github.io
  web documentation for Trinotate
  ☆48Updated 2 years ago
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…
  ☆106Updated 3 months ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• nf-core / smrnaseq
  A small-RNA sequencing analysis pipeline
  ☆94Updated 4 months ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆142Updated 2 months ago
• mritchielab / long_read_tools
  A catalogue of available long read sequencing data analysis tools
  ☆78Updated last week
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆82Updated 3 years ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆104Updated 4 months ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆150Updated last week
• louiejtaylor / grabseqs
  A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
  ☆107Updated last month
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• broadinstitute / catch
  A package for designing compact and comprehensive capture probe sets.
  ☆89Updated last year
• bcgsc / RNA-Bloom
  reference-free transcriptome assembly for short and long reads
  ☆109Updated last year
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆98Updated 2 years ago
• ExpressionAnalysis / ea-utils
  Automatically exported from code.google.com/p/ea-utils
  ☆96Updated 2 years ago
• ShiLab-Bioinformatics / subread
  The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon juncti…
  ☆47Updated 2 years ago
• CshlSiepelLab / phast
  PHAST
  ☆75Updated this week
• enasequence / enaBrowserTools
  A collection of scripts to assist in the retrieval of data from the ENA Browser
  ☆88Updated 2 months ago