Alternatives and similar repositories for fq

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

• fulcrumgenomics / fqgrep
  Grep for FASTQ files
  ☆97Updated last month
• sstadick / perbase
  Per-base per-nucleotide depth analysis
  ☆129Updated 4 months ago
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆56Updated 3 years ago
• fulcrumgenomics / fqtk
  Fast FASTQ sample demultiplexing in Rust.
  ☆62Updated last week
• brentp / jigv
  igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
  ☆127Updated last year
• brentp / echtvar
  using all the bits for echt rapid variant annotation and filtering
  ☆153Updated 2 months ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆96Updated last year
• google / best
  Bam Error Stats Tool (best): analysis of error types in aligned reads.
  ☆132Updated 3 months ago
• brentp / vcfexpress
  expressions on VCFs
  ☆85Updated last month
• tleonardi / nanocompore
  RNA modifications detection from Nanopore dRNA-Seq data
  ☆84Updated 2 weeks ago
• snakemake-workflows / dna-seq-varlociraptor
  A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, …
  ☆86Updated this week
• danrlu / nextflow_cheatsheet
  Tips for Nextflow and cheatsheet for channel operation
  ☆74Updated 9 months ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆140Updated last week
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆85Updated 6 years ago
• bentsherman / nf-boost
  Experimental features for Nextflow
  ☆43Updated 2 months ago
• compbiocore / VariantVisualization.jl
  Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
  ☆86Updated last year
• refgenie / refgenie
  Reference genome resource manager
  ☆76Updated last year
• wdecoster / cramino
  A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
  ☆151Updated 2 months ago
• nanoporetech / pinfish
  Tools to annotate genomes using long read transcriptomics data
  ☆45Updated 4 years ago
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆47Updated this week
• vsbuffalo / granges
  A Rust library and command line tool for working with genomic ranges and their data.
  ☆101Updated last year
• wdecoster / methplotlib
  Plotting tools for nanopore methylation data
  ☆93Updated last year
• nf-core / hlatyping
  Precision HLA typing from next-generation sequencing data
  ☆67Updated this week
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆104Updated this week
• NBISweden / pipelines-nextflow
  A set of workflows written in Nextflow for Genome Annotation.
  ☆45Updated 11 months ago
• jackh726 / bigtools
  A high-performance BigWig and BigBed library in Rust
  ☆90Updated last week
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆170Updated 11 months ago
• ChaissonLab / LRA
  Long read aligner
  ☆115Updated 2 years ago
• Kingsford-Group / scallop
  Scallop is a reference-based transcriptome assembler for RNA-seq
  ☆90Updated 4 years ago
• marcelm / dnaio
  Efficiently read and write sequencing data from Python
  ☆64Updated last week