Alternatives and similar repositories for parallel-fastq-dump

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

• Xinglab / rmats-turbo
  ☆286Updated 2 months ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆351Updated 3 weeks ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆257Updated 3 months ago
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆220Updated last month
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆251Updated last week
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆274Updated 2 months ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆348Updated last month
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆278Updated 2 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆262Updated 2 years ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆290Updated 2 months ago
• Boyle-Lab / Blacklist
  Application for making ENCODE Blacklists
  ☆333Updated 4 years ago
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆246Updated this week
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆217Updated last month
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆430Updated last year
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆268Updated 2 years ago
• CompEpigen / figeno
  Tool for plotting sequencing data along genomic coordinates.
  ☆335Updated last month
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆396Updated 2 months ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆362Updated this week
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆227Updated 6 months ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆395Updated this week
• wwood / kingfisher-download
  Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
  ☆286Updated 4 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
  ☆185Updated 3 weeks ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆440Updated 5 months ago
• nf-core / chipseq
  ChIP-seq peak-calling, QC and differential analysis pipeline.
  ☆229Updated last month
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆262Updated 5 months ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆218Updated 5 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆322Updated 3 years ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆245Updated 3 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆557Updated last year
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆198Updated 2 years ago