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...g the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (B...2878 days ago
- ...ties that should hold true for a correct assembly (e.g., mate-pairs are aligned at the correct distance fr...other in the assembly, the depth of coverage is fairly uniform along contigs, etc.). The violations of th...
2841 days ago
- ...file format, whereas the output format can be chosen among several formats. The application is especially optimized and adapted for the creation of high-quality, detailed circular m...
2878 days ago
- ...bsp;variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette ‘vcf data.’...
2875 days ago
- ...However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of sc...anscript evidence that suggests adjacency between scaffolds and contigs. Software requirements BLA...
2870 days ago
- ...e finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by signal, content and homology (pro...
2868 days ago
- ...ukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal s...ementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for a...
2009 days ago
- ...enomes.Program takes as input assembled contigs, paired-end and/or mate...total size smaller than the input contigs. In addition, Redundans will...tection and selectively removal of redundant contigs from an initial de novo...
2862 days ago
- ...sepairs in colour and to also visualize corresponding multiple sequence alignments and co-variation inform...chie, available for download and local use for more customized figures and scripting. http://ww...
2862 days ago
- ...in the world of sequencing. Merely five years back, genome sequencing of higher eukaryotes used to be very...the globe. Naturally, the capacities at those sequencing facilities were significantly constrained from hi...
2858 days ago
