Scripts and data regarding Vampyrellida genomics.
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Updated
May 13, 2024 - Shell
Scripts and data regarding Vampyrellida genomics.
a pacbiohifi analyzer for pacbiohifi reads from sequence analysis to the graph alignments
Fast and accurate de novo assembler for long reads
A snakemake workflow for de novo genome assembly. It produces chromosome-scale primary/phased assemblies complete of organelles (mitochondrion and/or chloroplast). It automatically assesses the quality of the results.
Pipeline for the identification of (coding) gene structures in draft genomes.
A program for assessing the T2T genome continuity
This repository contains a Python-based genome assembler designed to perform k-mer spectrum-based error correction and generate SAM files for visualizing genome mappings. It supports genomic data analysis with a focus on identifying mutations relevant to antibiotic resistance.
SPAdes Genome Assembler
Linear-time de novo Long Read Assembler
Implementation of ToL genome assembly workflows
Scripts and pipeine for Genome_assembly_annotation
De novo genome assembly of subset of the durian fruit genome.
The haplotype-resolved and T2T genome assembly of Solanum commersonii
Nextflow pipeline to assemble genomes from nanopore reads.
Modifies an assembly with sequencing reads to ensure all reads align end-to-end on the assembly
awk simulators for the pacbiohifi assembly reading from the graphs. easy to use awk for the coverage and the length files. udpating later on with the complete awk functionalities for the compilation into the direct kernels.
a combination of the gawk and the awk basic compiler to create a function that will estimate the aligned genome fractions from the paf alignment of the genome long reads to the genome. This includes multiple functions which also allow for the filtering of the quality alignments before estimating the genome length coverage.
a slurm configuration analytical pipline for the analysis of the pacbiohifi sequencing genomes using the verkko, hifiasm and the genomeasm4pg. only provide the link to the sequencing or the files with the folder and rest it will do the work
a genome reference estimation based on the peak size calibration and the given the values of the peak size calibration will estimate the genome and the sub genome fraction.
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