Alternatives and similar repositories for biofast:

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

• samuell / gccontent-benchmark
  Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)
  ☆57Updated 2 years ago
• OpenGene / SeqMaker.jl
  (No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
  ☆24Updated 7 years ago
• vibansal / HapCUT2
  software tools for haplotype assembly from sequence data
  ☆215Updated last week
• lh3 / cgranges
  A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
  ☆165Updated 8 months ago
• COMBINE-lab / pufferfish
  An efficient index for the colored, compacted, de Bruijn graph
  ☆107Updated 4 months ago
• marcelm / dnaio
  Efficiently read and write sequencing data from Python
  ☆61Updated 3 months ago
• brentp / slivar
  genetic variant expressions, annotation, and filtering for great good.
  ☆254Updated 8 months ago
• thegenemyers / FASTK
  A fast K-mer counter for high-fidelity shotgun datasets
  ☆123Updated last week
• smarco / WFA-paper
  Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
  ☆200Updated 2 years ago
• dpryan79 / libBigWig
  A C library for handling bigWig files
  ☆75Updated last month
• 38 / d4-format
  The D4 Quantitative Data Format
  ☆161Updated last week
• Ensembl / WiggleTools
  Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency
  ☆146Updated 3 months ago
• fulcrumgenomics / fqgrep
  Grep for FASTQ files
  ☆95Updated 3 weeks ago
• vcflib / bio-vcf
  Smart VCF parser DSL
  ☆82Updated 2 years ago
• waveygang / wfmash
  base-accurate DNA sequence alignments using WFA and mashmap3
  ☆182Updated this week
• lh3 / readfq
  Fast multi-line FASTA/Q reader in several programming languages
  ☆174Updated 3 years ago
• dpryan79 / MethylDackel
  A (mostly) universal methylation extractor for BS-seq experiments.
  ☆169Updated 8 months ago
• sstadick / perbase
  Per-base per-nucleotide depth analysis
  ☆125Updated last month
• varlociraptor / varlociraptor
  Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control.
  ☆122Updated this week
• ksahlin / strobemers
  A repository for generating strobemers and evalaution
  ☆77Updated 10 months ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆314Updated last year
• ekg / seqwish
  alignment to variation graph inducer
  ☆145Updated last week
• ChaissonLab / LRA
  Long read aligner
  ☆115Updated last year
• telatin / seqfu2
  seqfu - Sequece Fastx Utilities
  ☆113Updated last month
• GFA-spec / GFA-spec
  Graphical Fragment Assembly (GFA) Format Specification
  ☆205Updated 6 months ago
• Illumina / paragraph
  Graph realignment tools for structural variants
  ☆156Updated 2 years ago
• brentp / echtvar
  using all the bits for echt rapid variant annotation and filtering
  ☆148Updated 3 months ago
• brentp / jigv
  igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
  ☆126Updated last year
• stjude-rust-labs / fq
  Command line utility for manipulating Illumina-generated FASTQ files.
  ☆81Updated 3 weeks ago