Versatile genome assembly evaluation with QUAST-LG
QUAST-LG is an extension of QUAST intended for evaluating large-scale genome assemblies (up to mammalian-size). QUAST-LG is included in the QUAST ...1976 days ago
GenomeView: genome browser and annotation editor
...s reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.This project ha...1964 days ago
ZENBU: a collaborative, omics data integration and interactive visualization system
...sualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files. Please check our d...1962 days ago
MCAT: Motif Combining and Association Tool
This is a pipeline for finding motifs in fasta files.It can be run from the command line as follows: usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [...1953 days ago
DISTRUCT: a program for the graphical display of population structure
...load manual] [Download software note from Molecular Ecology Notes 4: 137-138 (2004)] To use the UNIX versions, unzip and untar the files in an appropriate directory u...1882 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...ces (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic...ulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations&m...1760 days ago
GffCompare: Program for processing GTF/GFF files
The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).1776 days ago
ALF--a simulation framework for genome evolution.
Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of...1671 days ago
Bioinformatics web development course
...ts of programming by using scripting languages: variables, types, arrays, cycles, conditional statements, functions, objects, regular expressions, files reading and manipulation et-c...1656 days ago
Minipolish: A tool for Racon polishing of miniasm assemblies
...polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs ...1629 days ago