Seal: SEquence ALignment evaluation suite
...several utilities that can be used to evaluate alignment algorithms, including: Reading a pre-existing reference genome from one or more FASTA files. Alternatively, generating a...2328 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 of all jobs in the system, and get bac...2322 days ago
GIGGLE: a search engine for large-scale integrated genome analysis
...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...2321 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 the separation of th...1581 days ago
2298 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
...We recommend BWA for mapping of the reads. When the mapping has been perfomed, the individuals need to be genotyped; SEX-DETector takes files produced by Reads2snp (which...2181 days ago
CrossMap: a program for convenient conversion of genome coordinates
CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm...2180 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...ker hits into complete TE copies, including LTR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics f...2176 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...ous in vivo cloning steps. Further information about fragScaff, including source code, is available at:https://sourceforge.net/projects/fragscaff/files. Manuscript describing fragS...2197 days ago
TULIP - The Uncorrected Long read Integration Pipeline
...re very much intended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long reads to sparse short...2196 days ago