Pinned Repositories
a-telomeric-repeat-database
A mass non-curated database of potential telomeric repeat sequences across the eukaryotic tree of life.
fasta_windows
A Rust implementation of sliding window stats over fastas.
fpma
Fast Plant Mito Annotation.
fw_plot
Create simple plots of fasta_windows output.
gfatk
A plant organellar Graphical Fragment Assembly toolkit
haplotype-windows
Calculate SNP density in sliding windows over a VCF.
plant-organellome-assembly
Automation of plant organelle assemblies from raw reads.
telomeric-identifier
Identify and find telomeres, or telomeric repeats in a genome.
tolkein
Tree of Life Kit of Evolutionary Informatics Novelties
vcf2msa
Given a VCF and a reference genome, create a multiple sequence alignment of the samples.
tolkit's Repositories
tolkit/telomeric-identifier
Identify and find telomeres, or telomeric repeats in a genome.
tolkit/gfatk
A plant organellar Graphical Fragment Assembly toolkit
tolkit/fasta_windows
A Rust implementation of sliding window stats over fastas.
tolkit/a-telomeric-repeat-database
A mass non-curated database of potential telomeric repeat sequences across the eukaryotic tree of life.
tolkit/fpma
Fast Plant Mito Annotation.
tolkit/haplotype-windows
Calculate SNP density in sliding windows over a VCF.
tolkit/vcf2msa
Given a VCF and a reference genome, create a multiple sequence alignment of the samples.
tolkit/fw_plot
Create simple plots of fasta_windows output.
tolkit/plant-organellome-assembly
Automation of plant organelle assemblies from raw reads.
tolkit/gff-stats
Calculate GC4 and GC3 from a gff and a fasta.
tolkit/tolkein
Tree of Life Kit of Evolutionary Informatics Novelties
tolkit/all-sequencing-status
A statement of the sequencing status of each species run through DToL.
tolkit/fasta_window_stats
Sequence patterns on fasta files.
tolkit/fppa
Fast Plant Plastid Annotation
tolkit/fw_group
Aggregate fasta_windows output.
tolkit/gff-rename
Replace sequence_IDs in gff3 based on given genome.fasta
tolkit/nemADSQ
A repository containing pipelines for nematode genome assembly, decontamination, scaffolding, and QC
tolkit/aa2nucaln
Amino acid to nucleotide alignment, as per this paper: https://academic.oup.com/bioinformatics/article/31/11/1836/2365396
tolkit/apple_day
Project progression & code for apple day 2021!
tolkit/BUSCO_karyotyping
Mapping BUSCO genes from a reference genome to a new assembly to quickly infer simple rearrangement events
tolkit/cgr
Chaos Game Representation of DNA sequences
tolkit/containerize-conda
Turn an existing conda environment into a Singularity container
tolkit/mblaxter_oscheius_genomes_sequencing
Draft genome assemblies and QC data
tolkit/nf-workshop
Nextflow workshop at the Sanger Institute
tolkit/otipu_chrom_assem
Scripts and files associated with the chromosomal assembly of O. tipulae manuscript
tolkit/samclip
Filter SAM file for soft and hard clipped alignments