Results for "Contigs"
Blogs
Tools to detect synteny blocks regions among multiple genomes
...dentifying and displaying genome synteny alignments. The genomes may be represented by sequenced chromosomes (pseudomolecules), by draft sequence contigs, or by FPC physical maps (wit...2605 days ago
String graph based genome assembly software and tools !
...rors in the reads. The second phase assembles contigs from the corrected reads. The...or mate pair data to build scaffolds from the contigs. The output of this software...Such consensus sequences are then extended to contigs. BASE is a practically e...2323 days ago
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Bookmarks
Scaffolding of a bacterial genome using MinION nanopore sequencing
...contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A...3219 days ago
- HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUS...
1087 days ago
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Pages
Genome Assembly Tools and Software - PART2 !!
...aset, it is capable of assembling contigs together to form more complet...0.2 – Assembly Alignment of ContigsSimAssemblyStage1: Perfectly a...a software that extends and joins contigs or scaffolds by reassembling...ntifies novel transfrags with DNA contigs or genes of close related spe...2680 days ago
Top-level pages
- ...ioinformatics tools are necessary to arrive from a raw DNA sequence at an annotated protein sequences: establish the correct order of sequence contigs to obtain one continuous sequ...
3942 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...ign without available reference. Willing et al., Bioinformatics 27(16):2187-93, 2011. Publisher Website Local de novo assembly of RAD paired-end contigs using short sequencing reads....3774 days ago
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Wire posts
News
Phased Human Genome Assembly !
...h more than half of the genome contained in gapless sequence at least 27 Mb long. The primary contig assembly is 2.89 Gb long and consists of 865 contigs that were assembled with PacB...2031 days ago
Bio-Scripts
- # generate dotplot lastdb test/ref.fa lastal -f TAB test/ref.fa test/contigs.reduced.pacbio.fa | last-dotplot - test/contigs.reduced.pacbio.fa.ref.png lastal -f TAB test/ref.fa test/contigs.reduced.nanopore.fa | last-dotplot - test/contigs.reduced.nanopore.fa.ref.png
2246 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
...BWA-sampe in one go. An example call for mapping with this script is python reads_to_ctg_map.py /path/to/lib1_A.fq /path/to/lib1_B.fq /path/to/contigs.fasta --threads N where N is...2119 days ago
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Tags
- Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for collections of contigs with a view to separating out th...
Tags: Bioinformatics, Blobsplorer, Visualization, Assembled DNA, Sequence, contigs, Species, Pools.
2876 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmi...Tags: npScarf, real-time, scaffolder, SPAdes, contigs, Nanopore, sequencing, reads
2150 days ago
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Comments
Comment on "Short-read assembly using Spades !"
...tput_dir> with the name of the output directory where the assembled contigs will be saved. Check the o...des has finished running, check the output directory for the assembled contigs. The contigs will be saved in...415 days ago
Comment on "REAPR: a universal tool for genome assembly evaluation"
...to each other. The program will also break up contigs/scaffolds at spurious sites to form smaller (but hopefully correct) contigs. Reapr runs pretty slowly, sa...nd you will get an assembly file with renamed contigs. Once the names are ok, we c...1331 days ago
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