3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes repor...pipeline uses tools and methods from Juicer (Durand &...al., Cell Systems, 2016) and Juicebox (Durand &...2372 days ago
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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...901 days ago
G-compass: a comparative genome browser
G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolutionarily conserved genomic regions between human and other 12...2267 days ago
SciLifeLab tutorial for bioinformatics analysis !
SciLifeLab is a national center for molecular biosciences with focus on health and environmental research. Courses Old courses (2012-2014) Metagenomics Workshop 2015 November - Uppsala...2262 days ago
Cerulean: A hybrid assembly using high throughput short and long reads
Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads u...mes in mind. The method is fully described in Deshpande, V., Fung, E. D., Pham, S., &...2213 days ago
LAMSA: fast split read alignment with long approximate matches
LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with...is open source and free for non-commercial use. LAMSA is mainly designed by Bo Liu &...2234 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads,...variants. If you use HapCUT2 in your research, please cite: Edge, P., Bafna, V. &...2234 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some i...bes the methods used for scaffolding. Ghurye, J., Pop, M., Koren, S., Bickhart, D., &...2203 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam #...2198 days ago