3386 days ago
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
2815 days ago
2768 days ago
Genome Assembly Tools and Software - PART2 !!
...liably order and orient sequence scaffolds generated by NGS and assembl...S (Repeat-masked Phrap with scaffolding), a WGS sequence assembler...cing reads and producing genomic scaffolds, open-reading frames and tax...; Generate Draft Genome Sequence Scaffolds for ProkaryotesSIS (Sca...2647 days ago
Awesome perl frameworks, libraries and software - PART 3
...ty/lua-upstream-nginx-module - Nginx C module to expose Lua API to ngx_lua for Nginx upstreams openresty/test-nginx - Data-driven test scaffold for Nginx C module and OpenRe...2456 days ago
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
RA Bioinformatics at School of Computational & Integrative Sciences, JNU, India
...lated experience is a necessary qualification proven by paper published and program developed. Desired Skills: Research experience in Chemical scaffold mapping, in silico Spectral a...2687 days ago
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
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
2761 days ago