BBTools for bioinformatician !
...gz --------------------------------------------------------------BBMerge.shBBMerge now has a new flag - "outa" o...cified. Usage: Code: $ dedupe.sh in=assembly1.fa,assembly2.fa out=merged.fa That will absorb exact...2259 days ago
Illumina based assembly pipeline steps !
Illumina Merge re-sequenced FastQ files (cat) Read QC (FastQC) Adapter trimming (fastp) Removal of host reads (Kraken 2; optional) Variant calling Read alignment (Bo...865 days ago
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
...bsp;is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized an...sitive results. Together with a highly optimized implementation, it can merge millions of paired end reads...2939 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 ord...2682 days ago
Evaluation of genome assembly software based on long reads
...r , SGA Assembler, Smartdenovo, Abruijn, Ra, DBG2OLC, Spades and Cerulean. The first 8 software use only long reads, while the 3 last software can merge long and short reads1908 days ago
Genome Assembly Tools and Software - PART2 !!
...into haplotypes. GAM-NGS 1.1b – Genome Assemblies Merger for Next Generation SequencingGAM-NGS is able to merge two or more assemblies and it...eads into new contigs; reference contigs are extended or merged; iterating the whole process...2674 days ago
Awesome perl frameworks, libraries and software - PART 3
...lence/electron GUI toolkit erinspice/geni-automerge - A tool written in Perl using the Geni.com API which automatically merges sufficiently similar profile...and OpenResty Lua library development mndrix/merge-this - Revision control...2482 days ago
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WuXi has acquired NextCODE Health
...extCODE Health, a genomic analysis and bioinformatics company based in the USA.The acquisition was made for $65 million in cash, and WuXi plans to merge its genome center with NextCO...3382 days ago
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Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2113 days ago
2111 days ago
CISA: Contig Integrator for Sequence Assembly
A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in order to generate the most optimal assembly. Howev...Tags: Bioinformatics, CISA, Assembly, Genome, Merger, Merge, CrossCompare
2686 days ago
GARM:Genome Assembly, Reconciliation and Merging
The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux distributions. The method merges contigs or scaf...Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, Merge, GARM
2682 days ago