Results for "Scaffold"

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Blogs

  • BBTools for bioinformatician !

    ...verage coverage (decimal point is allowed).metagenome will assign each scaffold a random exponential variable, which decides the probability that a read be generated from that scaffold. So, if you concatenate toget...

    2232 days ago

Bookmarks

  • WiseScaffolder

    Function WiseScaffolder is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs u...ta. It also produces editable scaffold maps, allowing either to buil...for the manual improvement of scaffolds scaffold constitutes the cen...

    2815 days ago

  • Ka, Ks and Ka/Ks calculations

    ...codons to compute the substitution rates (Ka, Ks and Ka/Ks) between a well-annotated genome and a non-annotated genome or even a poorly assembled scaffold dataset. It is especially use...

    2768 days ago

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Top-level pages

  • Genome Assembly Tools and Software - PART1 !!

    ...1.1.0 – Transcriptome Post Scaffolding TransPS is a pipeline f...ame gene of reference genome are scaffolded into one contig. ...ome and assembled sequence. Scaffold_builder v2.2 – Order Co...to automatically break incorrect scaffolds and flag other errors in an...

    2647 days ago

  • LINKS scaffolder bloomfilter setting !

    ...in git:(master) ✗ ./LINKS Usage: ./LINKS [v1.8.6] -f sequences to scaffold (Multi-FASTA format, required...CAGACGAC -d distance between k-mer pairs (ie. target distances to re-scaffold on. default -d 4000, optional...

    2113 days ago

Opportunity posts

Bio-Scripts

  • Create genome scaffolding with Perl

    ...RSION = "1.00"; =head1 NAME psl_scaffolder.pl - use self-mapped PSL file to scaffold a genome =head1 SYNOPSIS...query sequences "prefix" => "psl_scaffold_", # prefix for contig names...for (my $i = 0; $i {"prefix"}, $nextScaffoldID++); if(!exists($repl...

    2270 days ago

  • Perl script to break the contigs by 'N'

    ...g sequence my $seq = $seqobj->seq; my $lenseq=length $seq; $seq = uc $seq; #now all bases are in uppercase #Searches for NNNNN regions (scaffold breaks) #Hash nregions stor...

    2025 days ago

Tags

  • CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies

    CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license. Main features: works with any number of scaffold assemblies in de-novo non-progressive f...

    Tags: CAMSA, tool, Comparative, Analysis, Merging, Scaffold, Assemblies

    2282 days ago

  • SALSA: A tool to scaffold long read assemblies with Hi-C

    This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA m...

    Tags: SALSA, tool, scaffold, long, read, assemblies, Hi-C, Genome

    2113 days ago

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Comments

  • Comment on "Platanus"

    ...ate-pair) data and constructs scaffolds. Finally, paired-end reads localized on gaps in scaffolds are assembled and gaps are c...gt;ass_log.txt > platanus scaffold -c out_contig.fa -b out_conti...and makes scaffolds, then decreases the threshol...

    2761 days ago