Referee: Genome assembly quality scores
...types (AA, AC, AG, AT, CC, CG, CT, GG, GT, TT). Referee takes as input the genotype likelihoods calculated for all 10 genotypes given the called reference base at each position. Refer...2060 days ago
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
...lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher...2038 days ago
KEGG Mapper – Reconstruct Pathway
...ins the user-defined gene identifier followed by, if any, the assigned K number. The mapping is performed through the K numbers against the KEGG reference pathways.2023 days ago
2023 days ago
Genome Annotation using MAKER tutorial !
MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice...2014 days ago
Versatile genome assembly evaluation with QUAST-LG
...inimap2) and the refactoring of alignment analyzing modules New k-mer-based completeness and correctness metrics BUSCO added for enhanced reference-free analysis The concept of...2013 days ago
GenomeView: genome browser and annotation editor
GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are su...2002 days ago
SvABA: Genome-wide detection of structural variants and indels by local assembly
...is can be customized to any set of reads at the command line using VariantBam rules. These contigs are then immediately aligned to the reference with BWA-MEM and parsed to id...1982 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
...ved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence. For further...1955 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...oodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft g...s into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this too...1896 days ago