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...2619 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...2337 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...3233 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...
1101 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...2694 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...
3956 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....3788 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...2045 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
2261 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...2133 days ago
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Tags
Gap filling or Contigs extensions tools !
There are many tools to perform gap filling using Illumina short reads, for example "GapFiller: a de novo assembly approach to fill the gap within paired reads" or "Toward almost closed genomes with GapFiller". There are also some tools like GAPresolution that can help to perform local re-assembl...Tags: Gap, filling, Contigs, extensions, tools
2174 days ago
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...429 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...1346 days ago
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