Alternatives and similar repositories for fastq_utils:

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

• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆59Updated 6 months ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆49Updated 4 years ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆61Updated last year
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆47Updated 2 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆96Updated last year
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 4 years ago
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆25Updated 2 months ago
• jlab-code / MethylStar
  A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
  ☆35Updated 3 years ago
• shimlab / BLAZE
  SingleCell Nanopore sequencing data analysis
  ☆57Updated 4 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆85Updated 6 years ago
• adamewing / tebreak
  Find and characterise transposable element insertions
  ☆21Updated last year
• AndreasHeger / gat
  Genomic Association Tester
  ☆31Updated last year
• refgenie / refgenie
  Reference genome resource manager
  ☆76Updated last year
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆80Updated 2 months ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated 9 months ago
• stephenfloor / extract-transcript-regions
  For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…
  ☆35Updated last year
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆39Updated last month
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆53Updated 6 months ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆46Updated this week
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆108Updated 4 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆55Updated 2 years ago
• rrazaghi / modbamtools
  Set of tools to manipulate and visualize modified base bam files
  ☆54Updated 2 years ago
• zavolanlab / zarp
  The Zavolab Automated RNA-seq Pipeline
  ☆35Updated this week
• christopher-vollmers / Mandalorion
  Pipeline to identify isoforms from full-length cDNA sequencing data
  ☆24Updated 11 months ago
• Shians / NanoMethViz
  ☆27Updated last week
• nanoporetech / pipeline-pinfish-analysis
  Pipeline for annotating genomes using long read transcriptomics data with pinfish
  ☆27Updated 4 years ago
• jsh58 / NGmerge
  Merging paired-end reads and removing adapters
  ☆44Updated last month
• LHentges / LanceOtron
  ☆27Updated 8 months ago
• khuang28jhu / bs3
  BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
  ☆27Updated 5 years ago