“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...genome coverage...) Ambiguous cases such as nested TE can be assembled into copies automatically or manually Allow for working with a TE user-defined library Allow for working with only a user-chosen set o...2189 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
...bled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an issue for downstream analysis whether you're working on the haploid or phased-dipl...1993 days ago
Biotite: A general framework for computational biology
...se on the one hand side, but is also computationally efficient due to intensive usage of NumPy and Cython. This package focuses on working with sequence and structure d...1993 days ago
Bioinformatics web development course
...his web development course, targeted at Biology and Bioinformatics students, aims at teaching from scratch all the skills needed to setup a fully working Linux web server and to devel...1669 days ago
Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo: https://vgteam.github.io/sequenceTubeMap/1544 days ago
Best Practices for Variant Calling with the GATK
...otyping Sheila Chandran PDF Video 03/19/15 Variant quality score recalibration Bertrand Haas PDF Video 03/19/15 Introduction to working with variants Yossi Farjoun...1561 days ago
Genobuntu: Package for Next Generation Sequencing and Genome Assembly
...also act as a good teaching source for a class room setting.Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assemb...1475 days ago
CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
...imilarity searches, codon alignments to Ka/Ks calculations and synteny. The new R package targets ecology, population and evolutionary biologists working in the field of comparative g...1298 days ago
Kmer: a suite of tools for DNA sequence analysis
...ies. Optimized for high-throughput batched alignment. LEAFF: LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In ad...1019 days ago