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GARM:Genome Assembly, Reconciliation and Merging
...ine is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al.,...eline was tested on Debian, Ubuntu, Fedora and BioLinux distributions....ocess of finding probable compressions or extensions (CE) problems in t...2749 days ago
GAM-NGS: genomic assemblies merger for next generation sequencing
GAM-NGS (Genomic Assemblies Merger for Next Generation Sequencing), whose primary goal is to merge two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does...mic locus (called blocks) are identified through reads' al...2749 days ago
- PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilob...red-end read overlaps and without requiring the target fragment s...in a couple of minutes on a standard desktop computer.
2749 days ago
MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs
MeGAMerge MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing...) Description MeGAMerge is a perl based wrapper/tool that can...s of any length in Multi-FASTA format to produce an improved con...g tools installed and in $PATH, or added to $binpath in the tool...2749 days ago
- quickmerge uses a simple concept to improve contiguity of genome assemblies...ng molecule sequences, often with dramatic outcomes. The program u...m assemblies made with illumina short reads and PacBio long reads...ort reads are not typically considered to cover genomic regions wh...
2749 days ago
- ...andle big sequence data, e.g: Compare two vertebrate genomes Align billion...of DNA reads to a genome Indicate the reliability of each aligne...ences Calculate the likelihood of chance similarities between random sequences...
2748 days ago
- pyScaf orders contigs from genome assemblies utilising several types of information: paired-end (PE) and/or mate-pair libraries (NGS-base...nome of some related species (reference-based mode) Scaffo...econstructing correctly all chromosomes always for CANPA and...
2748 days ago
- If genomes were completely random sequences in a statistical sense, 'overlap-consensus-layout' method would have been enough to assemble large genomes from Sanger reads....s, and they are hard to assemble using overlap-consensus-layout approach....
2748 days ago
- MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors....easy-to-use and quick way to identify conserved gene arrays both within th...
2746 days ago
Finding Patterns in Biological Sequences
In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and...ly we list publicly available tools and databases for pattern discovery. On-line su...2746 days ago
