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 reported in: Dudchenko et al., De novo assembly of the Aedes aegypti genome using Hi-C yi...2347 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and pl...2216 days ago
WhatsHap: fast and accurate read-based phasing
...acBio, Oxford Nanopore and other types of reads It phases SNVs, indels and even “complex” variants (such as TCG → AGAA) Pedigree phasing mode uses...2196 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
Quality assessment of this mRNA Transcript Assembly Software is described in EvidentialGene_quality. Too many transcript assemblies is much better than too few....2070 days ago
Referee: Genome assembly quality scores
...We accomplish this by first calculating genotype likelihoods for every site. For a given site in a diploid genome, there are 10 possible genotypes (AA, AC, AG, AT, CC, CG, CT, GG,...2036 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
...marks kallisto significantly outperforms existing tools. kallisto is described in detail in: Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pacht...1972 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automa...1930 days ago
1589 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
...alignments. More at https://github.com/ekg/glia glia -f ~/human_g1k_v37.fasta -t 20:62900077-62902077 -v variants.vcf.gz \ -s AAATGTAAACATTTTATAGGGGATTCCCCTAAAAACAA...1586 days ago
3D de novo assembly (3D DNA) pipeline
...p;Genome Assembly Cookbook on http://aidenlab.org/assembly. For the original version of the pipeline and to reproduce the Hs2-HiC and the AaegL4 genomes reported in ...1581 days ago