NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captur...nment-based analysis and generates a set of read profiles serving as the input to the n...ome. NanoSim is written in Python and R. The source files and manual are available at t...2343 days ago
Rectangle Graph for Repeat Resolution in Genome Assembly
Ultimate tool for resolving repeats in genome assemblies. Though the specific impl...can be run with other genome assemblers if they use the graph format as SPAdes files. For more details see: Nikol...2333 days ago
Seal: SEquence ALignment evaluation suite
Seal is a comprehensive sequencing simulation and alignment tool evaluation su...s, including: Reading a pre-existing reference genome from one or more FASTA files. Alternatively, generating a...2327 days ago
Frontend: Perl Web framework documentation - Andrej Sali Lab
The frontend is a set of Perl classes that displays the web interface, allowing a user to upload their input files, start a job, display a list...2321 days ago
GIGGLE: a search engine for large-scale integrated genome analysis
GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/r...2320 days ago
RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as t...1580 days ago
2297 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), an...862 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (par...ing has been perfomed, the individuals need to be genotyped; SEX-DETector takes files produced by Reads2snp (which...2180 days ago
CrossMap: a program for convenient conversion of genome coordinates
...a program for convenient conversion of genome coordinates (or annotation files) between different assembli...pports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. CrossMap is d...2179 days ago