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
  ☆94Updated last month
• tleonardi / nanocompore
  RNA modifications detection from Nanopore dRNA-Seq data
  ☆81Updated 11 months ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆92Updated 9 months 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, …
  ☆83Updated this week
• sstadick / perbase
  Per-base per-nucleotide depth analysis
  ☆122Updated this week
• brentp / jigv
  igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
  ☆126Updated last year
• google / best
  Bam Error Stats Tool (best): analysis of error types in aligned reads.
  ☆126Updated 10 months ago
• fulcrumgenomics / fqtk
  Fast FASTQ sample demultiplexing in Rust.
  ☆58Updated last month
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆110Updated 3 weeks ago
• GeneDx / pgr-tk
  PGR-TK: Pangenome Research Tool Kit
  ☆96Updated 8 months ago
• brentp / vcfexpress
  expressions on VCFs
  ☆66Updated 3 months ago
• bioinformatics-centre / BayesTyper
  A method for variant graph genotyping based on exact alignment of k-mers
  ☆87Updated 5 years ago
• ChaissonLab / LRA
  Long read aligner
  ☆114Updated last year
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆137Updated 7 months ago
• nanoporetech / pinfish
  Tools to annotate genomes using long read transcriptomics data
  ☆45Updated 4 years ago
• vsbuffalo / granges
  A Rust library and command line tool for working with genomic ranges and their data.
  ☆101Updated 7 months ago
• COMBINE-lab / oarfish
  long read RNA-seq quantification
  ☆73Updated this week
• brentp / echtvar
  using all the bits for echt rapid variant annotation and filtering
  ☆147Updated 2 months ago
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆57Updated 3 years ago
• mourisl / T1K
  T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.
  ☆59Updated last week
• LooseLab / bulkvis
  ☆46Updated 2 months ago
• nf-core / isoseq
  Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed …
  ☆32Updated this week
• compbiocore / VariantVisualization.jl
  Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
  ☆85Updated last year
• cortes-ciriano-lab / savana
  Somatic structural variant caller for long-read data
  ☆53Updated this week
• broadinstitute / viral-pipelines
  viral-ngs: complete pipelines
  ☆61Updated this week
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆100Updated this week
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆84Updated 6 years ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆57Updated 3 months ago
• refgenie / refgenie
  Reference genome resource manager
  ☆73Updated last year
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated 3 months ago