jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...ts can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent s...and optical/PCR duplicates. All outputs can be written to standard file formats. A swift, versatile phyloge...1754 days ago
Kalign: fast multiple sequence alignment program for biological sequences.
...biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal format: kalign -i BB11001.tfa -f cl...1657 days ago
GfaViz: flexible and interactive visualization of GFA sequence graphs
GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence...1573 days ago
BlobToolKit: A toolkit for genome assembly QC
...2 and/or visualised in the Viewer. The BlobToolKit Specification features a formal schema and validator for the JSON-based BlobDir format used by BlobTools2 ...1544 days ago
shinyChromosome:a GUI for the interactive creation of non-circular whole genome diagrams
...menu. To cretae two-genome plot for comparison of data across two genomes, go to the Two-genome plot menu. For the detail format of input data, check the Input data format submenu of the Help menu. sh...1536 days ago
SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.
...nX for the same input query. Optional track file in bedgraph format to annotate the generated cha...o download the generated visualizations in publication ready SVG or PNG formats.1444 days ago
parallelLastz: Lastz with multi-threads support.
...g Lastz (https://github.com/lastz/lastz) in parallel mode. This program is for single computer with multiple core processors. When the query file format is fasta, you can specify man...1361 days ago
maftools : Summarize, Analyze and Visualize MAF Files
...s in Cancer Genomics, Mutation Annotation Format (MAF) is being widely ac...stored in the form of Mutation Annotation Format. This package attempts to sum...in-house studies as long as the data is in MAF format.1238 days ago
Pandoc: The universal markup converter
Pandoc is a Haskell library for converting from one markup format to another, and a command-line tool that uses this library. Pandoc is a free and open-source document converter, widely used as a writing tool and as a basis for publishing workflows. More at https://pandoc.org/1212 days ago
FiNGS: Filters for Next Generation Sequencing
...is simple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot int...1172 days ago