Alternatives and similar repositories for fqtk

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

• vsbuffalo / granges
  A Rust library and command line tool for working with genomic ranges and their data.
  ☆100Updated last year
• adnaniazi / tailfindr
  An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
  ☆54Updated last year
• ArcInstitute / xsra
  An efficient CLI to extract sequences from the SRA
  ☆114Updated this week
• pachterlab / splitcode
  Flexible and efficient parsing, interpreting and editing of sequencing reads
  ☆44Updated last week
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆98Updated last year
• noamteyssier / bedrs
  bedtools-like functionality for interval sets in rust
  ☆54Updated 2 months ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆64Updated last year
• huangnengCSU / longcallR
  LongcallR is a SNP caller for single molecule long-read RNA-seq data
  ☆67Updated last month
• quinlan-lab / bedder-rs
  an API for intersections of genomic data
  ☆74Updated this week
• rhpvorderman / sequali
  Fast sequencing data quality metrics
  ☆28Updated last month
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆63Updated 5 months ago
• COMBINE-lab / oarfish
  long read RNA-seq quantification
  ☆91Updated last week
• lh3 / ref-gen
  Human reference genome analysis sets
  ☆55Updated 2 years ago
• nf-core / variantbenchmarking
  Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
  ☆36Updated this week
• refgenie / refgenie
  Reference genome resource manager
  ☆74Updated last year
• jsh58 / NGmerge
  Merging paired-end reads and removing adapters
  ☆46Updated last month
• telatin / covtobed
  ⛰ covtobed | Convert the coverage track from a BAM file into a BED file
  ☆44Updated 4 months ago
• alejandrogzi / gtfsort
  a lexicographically-based GTF/GFF sorter
  ☆35Updated 6 months ago
• sandberg-lab / Spreading-Correction
  Supplementary information to "Computational correction of index switching in multiplexed sequencing libraries" (Larsson et. al 2018).
  ☆15Updated 4 years ago
• YingZhou001 / Immuannot
  Immuological gene typing and annotation for genome assembly
  ☆38Updated 7 months ago
• OceanGenomics / mudskipper
  A tool for projecting genomic alignments to transcriptomic coordinates
  ☆36Updated last year
• fulcrumgenomics / fqgrep
  Grep for FASTQ files
  ☆98Updated 6 months ago
• harvardinformatics / NGmerge
  Merging paired-end reads and removing adapters
  ☆30Updated 5 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆142Updated 2 months ago
• nextflow-io / nf-validation
  Params validation plugin for Nextflow pipelines
  ☆48Updated last year
• derijkp / scywalker
  A program for the analysis of single cell nanopore long read data
  ☆19Updated 3 months ago
• ksahlin / ultra
  Long-read splice alignment with high accuracy
  ☆63Updated last year
• drostlab / myTAI
  Evolutionary Transcriptomics with R
  ☆46Updated 2 weeks ago
• zavolanlab / zarp
  The Zavolab Automated RNA-seq Pipeline
  ☆35Updated 3 months ago
• mribeirodantas / NextflowSnippets
  This repository hosts a large collection of Nextflow snippets
  ☆56Updated 9 months ago