Results for "script"
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Generate interactive codon usage plots
Generate interactive codon usage plots as used at ensembl.lepbase.org. The input file format can be generated from an Ensembl database using the export_json.pl script from the easy-import pipeline. live demo2254 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...t of K-mer histograms that are derived from selected rows or columns in a matrix produced by the "comp". In addition, KAT contains a python script for analysing the mathematica...1977 days ago
- ...post assembly tools. Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit...
1968 days ago
dotPlotly: Generate an interactive dot plot from mummer or minimap alignments
Create an interactive dot plot from mummer output OR PAF format R script that makes a plotly interactive and/or static (png/pdf) dot plot. Shiny app available for testing1896 days ago
- CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).
1671 days ago
MGSE: Mapping-based Genome Size Estimation
...enome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly. The script construct_cov_file.py (https:...1566 days ago
SeqMule: Automated human exome/genome variants detection
SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file.1534 days ago
Genobuntu: Package for Next Generation Sequencing and Genome Assembly
....Commonly used biological software and example script files for different assembly...nes have also been provided, where the example script files can be updated to suit...NGS Reads Simulator HiTEC, FASTQC Minimum Description Length SOAPaligner Seque...1443 days ago
chromatiblock: Scalable, whole-genome visualisation of structural changes in prokaryotes
...atiblock you can reactivate this environemtn using conda activate chromatiblock Direct download: Alternatively you can download and run the script from here.1346 days ago
QuasR: Quantification and annotation of short reads in R
...high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification. A single R script can contain all steps of a co...992 days ago
