Alternatives and similar repositories for parallel-fastq-dump

Users that are interested in parallel-fastq-dump are comparing it to the libraries listed below

• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆201Updated 3 weeks ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆266Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆241Updated 2 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆308Updated 4 years ago
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆224Updated this week
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆265Updated 2 years ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆251Updated 4 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆211Updated last month
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆406Updated last year
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated 2 weeks ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆330Updated 2 months ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆136Updated 10 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆289Updated 8 months ago
• usadellab / Trimmomatic
  ☆248Updated last year
• Xinglab / rmats-turbo
  ☆260Updated 6 months ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆217Updated 2 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆167Updated this week
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 10 months ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 5 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆214Updated last month
• ENCODE-DCC / rna-seq-pipeline
  ☆151Updated 2 years ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆329Updated 3 months ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆275Updated 11 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆230Updated 4 years ago
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆215Updated this week
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆249Updated 6 months ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆228Updated this week