ccb.jhu.edu - 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).
sourceforge.net - Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from...
github.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences.
I made Rebaler for bacterial genomes (specifically for the...
gitlab.mbb.univ-montp2.fr - CroCo is a program to detect cross contamination events in assembled transcriptomes using sequencing reads to determine the true origin of every transcripts.Such cross contaminations can be expected if several RNA-Seq experiments were prepared...
github.com - Turn (almost) any Python command line program into a full GUI application with one line
The easiest way to install Gooey is via pip
pip install Gooey
Alternatively, you can install Gooey by cloning the project to your local directory
git...
crossmap.sourceforge.net - CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats...
bioinformatics.ua.pt - Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For...
www.broadinstitute.org - Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation...
harvest.readthedocs.io - Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.
Tools
Parsnp - Core-genome...
www.australianprostatecentre.org - Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom...