Jit
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CABOG: Celera Assembler with Best Overlap Graph
By Abhimanyu Singh 2760 days agowww.jcvi.org - CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as...
Run miniasm assembler on nanopore reads !
Last updated 2543 days ago by Jit Comments (5)Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...Scallop: reference-based transcriptome assembler for RNA-seq
By Rahul Nayak 2402 days agogithub.com - Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be...Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2238 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2...RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
By Jit 1797 days agoftp.genomics.org.cn - RePS (Repeat-masked Phrap with scaffolding), a WGS sequence assembler, that explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error...HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 1676 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
By Rahul Nayak 2179 days agobitbucket.org - Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...Genome Annotation
By Manshi Raghubanshi 4119 days agoDr. Rob Edwards describes some of the problems, challenges, and approches in genome annotation, with a particular emphasis on how the Fellowship for the Interpretation of Genomes (FIG) developed subsystems using the SEED database available at...Pollux: platform independent error correction of single and mixed genomes
By Jit 2756 days agogithub.com - Pollux: General-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and...Understanding liftOver !
By Rahul Nayak 2373 days agoLiftOver is a necesary step to bring all genetical analysis to the same reference build.
