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    26 repositories

    • gfatk

      Public
      A plant organellar Graphical Fragment Assembly toolkit
      Rust
      •
      MIT License
      •2•16•3•0•Updated Oct 11, 2024Oct 11, 2024

    • telomeric-identifier

      Public
      Identify and find telomeres, or telomeric repeats in a genome.
      rustgenomerepeatstelomerestelomerictelomerebioinformatics
      Rust
      •
      MIT License
      •12•111•5•1•Updated Oct 3, 2024Oct 3, 2024

    • nemADSQ

      Public
      A repository containing pipelines for nematode genome assembly, decontamination, scaffolding, and QC
      Nextflow
      •
      MIT License
      •3•1•1•0•Updated Sep 14, 2023Sep 14, 2023

    • fasta_windows

      Public
      A Rust implementation of sliding window stats over fastas.
      Rust
      •
      MIT License
      •2•13•2•0•Updated Jun 21, 2023Jun 21, 2023

    • containerize-conda

      Public
      Turn an existing conda environment into a Singularity container
      Python
      •14•0•0•0•Updated Mar 13, 2023Mar 13, 2023

    • gff-stats

      Public
      Calculate GC4 and GC3 from a gff and a fasta.
      bioinformatics
      Rust
      •
      MIT License
      •1•2•3•0•Updated Feb 2, 2023Feb 2, 2023

    • a-telomeric-repeat-database

      Public
      A mass non-curated database of potential telomeric repeat sequences across the eukaryotic tree of life.
      Shell
      •1•6•1•0•Updated Jan 22, 2023Jan 22, 2023

    • tolkein

      Public
      Tree of Life Kit of Evolutionary Informatics Novelties
      Python
      •
      MIT License
      •1•2•1•0•Updated Jul 12, 2022Jul 12, 2022

    • otipu_chrom_assem

      Public
      Scripts and files associated with the chromosomal assembly of O. tipulae manuscript
      Shell
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Jul 8, 2022Jul 8, 2022

    • plant-organellome-assembly

      Public
      Automation of plant organelle assemblies from raw reads.
      Python
      •0•3•0•0•Updated Jun 20, 2022Jun 20, 2022

    • fppa

      Public
      Fast Plant Plastid Annotation
      Rust
      •0•1•1•0•Updated Jun 13, 2022Jun 13, 2022

    • fpma

      Public
      Fast Plant Mito Annotation.
      Rust
      •0•7•1•0•Updated Jun 13, 2022Jun 13, 2022

    • aa2nucaln

      Public
      Amino acid to nucleotide alignment, as per this paper: https://academic.oup.com/bioinformatics/article/31/11/1836/2365396
      Rust
      •0•0•0•0•Updated Jun 6, 2022Jun 6, 2022

    • all-sequencing-status

      Public
      A statement of the sequencing status of each species run through DToL.
      Python
      •0•1•0•0•Updated Feb 22, 2022Feb 22, 2022

    • apple_day

      Public
      Project progression & code for apple day 2021!
      HTML
      •0•0•0•0•Updated Jan 28, 2022Jan 28, 2022

    • gff-rename

      Public
      Replace sequence_IDs in gff3 based on given genome.fasta
      Python
      •
      MIT License
      •1•1•0•0•Updated Nov 12, 2021Nov 12, 2021

    • vcf2msa

      Public
      Given a VCF and a reference genome, create a multiple sequence alignment of the samples.
      Rust
      •
      MIT License
      •0•7•0•0•Updated Oct 5, 2021Oct 5, 2021

    • fw_group

      Public
      Aggregate fasta_windows output.
      R
      •
      MIT License
      •0•1•0•0•Updated Jul 25, 2021Jul 25, 2021

    • fw_plot

      Public
      Create simple plots of fasta_windows output.
      Rust
      •
      MIT License
      •0•4•4•0•Updated Jun 10, 2021Jun 10, 2021

    • cgr

      Public
      Chaos Game Representation of DNA sequences
      Rust
      •0•0•0•0•Updated May 16, 2021May 16, 2021

    • haplotype-windows

      Public
      Calculate SNP density in sliding windows over a VCF.
      Rust
      •
      MIT License
      •0•8•0•0•Updated Mar 4, 2021Mar 4, 2021

    • BUSCO_karyotyping

      Public
      Mapping BUSCO genes from a reference genome to a new assembly to quickly infer simple rearrangement events
      Python
      •1•0•0•0•Updated Mar 3, 2021Mar 3, 2021

    • mblaxter_oscheius_genomes_sequencing

      Public
      Draft genome assemblies and QC data
      0•0•0•0•Updated Mar 1, 2021Mar 1, 2021

    • fasta_window_stats

      Public
      Sequence patterns on fasta files.
      JavaScript
      •0•1•0•0•Updated Jan 26, 2021Jan 26, 2021

    • samclip

      Public
      Filter SAM file for soft and hard clipped alignments
      Perl
      •
      GNU General Public License v3.0
      •10•0•0•0•Updated Jan 6, 2021Jan 6, 2021

    • nf-workshop

      Public
      Nextflow workshop at the Sanger Institute
      Shell
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Aug 24, 2020Aug 24, 2020