Alternatives and similar repositories for strainFlye:

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

• DaehwanKimLab / seqwho
  SeqWho - A reliable and rapid FASTQ(A) file classifier
  ☆11Updated 3 years ago
• bede / seqsum
  Robust individual and aggregate checksums for nucleotide sequences
  ☆16Updated last year
• pierrepeterlongo / kmer2sequences
  Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.
  ☆21Updated last year
• pg-space / panspace
  Embedding-based indexing for compact storage, rapid querying, and curation of bacterial pan-genomes
  ☆9Updated 2 weeks ago
• prophyle / prophasm
  ProphAsm – a rapid computation of simplitigs directly from k-mer sets
  ☆26Updated 2 years ago
• abs-tudelft / variant-calling-at-scale
  Scalable and High Performance Variant Calling on Cluster Environments
  ☆10Updated 3 years ago
• xa6xa6 / metaOthello
  ☆16Updated 6 years ago
• AllTheBacteria / Phylign
  Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…
  ☆12Updated 10 months ago
• vsbuffalo / hgindex
  Hierarchical binned indexed data store for on-disk genomic data.
  ☆14Updated 2 months ago
• uio-bmi / NucMerge
  Genome assembly quality improvement assisted by alternative assemblies and paired-end Illumina reads
  ☆7Updated 6 years ago
• Shamir-Lab / Faucet
  This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye R…
  ☆18Updated 7 years ago
• CAMI-challenge / second_challenge_evaluation
  Repository for codes, analyses and visualizations for the CAMI II challenges
  ☆11Updated last year
• xmuyulab / Snipe
  Highly sensitive pathogen detection
  ☆12Updated 4 years ago
• Singular-Genomics / singular-demux
  Singular Genomics Demultiplexing Tool
  ☆16Updated last year
• iqbal-lab-org / minos
  Variant call adjudication
  ☆16Updated 9 months ago
• aesheppard / TETyper
  transposable element typing pipeline
  ☆17Updated last year
• HKU-BAL / Translocator
  Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long read…
  ☆13Updated 5 years ago
• jsevo / taxumap
  ☆16Updated last year
• mreppell / Karp
  Accurate and fast taxonomic classification using pseudoaligning
  ☆21Updated 7 years ago
• althonos / pyfastani
  Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
  ☆22Updated 2 weeks ago
• kevsilva / StrainFLAIR
  Strain-level abundances estimation in metagenomic samples using variation graphs
  ☆25Updated 2 years ago
• ban-m / jtk
  JTK -- a regional diploid genome assembler
  ☆24Updated 5 months ago
• SilvioWeging / kASA
  kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding
  ☆23Updated last year
• edawson / svaha2
  Linear-time, low-memory construction of variation graphs
  ☆20Updated 5 years ago
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆21Updated 6 months ago
• ekg / wflign
  the we-flyin WFA-guided ultralong tiling sequence aligner
  ☆11Updated 3 years ago
• sanger-pathogens / panito
  Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment
  ☆16Updated 6 years ago
• lh3 / gfa1
  This repo is deprecated. Please use gfatools instead.
  ☆16Updated 6 years ago
• ChaissonLab / hmcnc
  Hidden Markov Model based Copy number caller
  ☆20Updated 5 months ago
• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆14Updated 6 months ago