Search Results for "assembler"

...This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used. Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss.

-------- ATTENTION START: RENAMING muda.pl was renamed to MANTI.pl with v3.7, project development can be tracked on the MANTI project page on sourceforge.net. Old versions remain here for archival purposes. -------- ATTENTION END muda.pl is an evaluation script (written in Perl) without great dependencies. It congregates information from 4 different MaxQuant output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data...

---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. ...

Meta Assembler for de novo assembly results. GARM (Genome Assembly Reconciliation and Merging) is a pipeline to merge results from different assemblers or results from different DNA sequencing technologies.

Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.

...A nucleotide assembly-based strategy does not fare much better since metagenomic assemblies are typically very fragmented and also leave a large fraction of reads unassembled. We present a method for reconstructing complete protein sequences directly from NGS metagenomic data. Our framework is based on a novel Short Peptide Assembler (SPA) that assembles protein sequences from their constituent peptide fragments identified on short reads. We also present a new implementation of SPA based on suffix array (SFA-SPA) which runs significantly faster than SPA. Youngik Yang, Cuncong Zhong, and Shibu Yooseph* J. Craig Venter Institute, San Diego, CA {yyang,czhong,syooseph}@jcvi.org * Corresponding author SPA is available in binary on 64 bit Linux OS. ...

...Later versions of TraceTuner, which support mixed base calling, have been used by the research community, the private biotech sector, and the U.S. government as components of different variant detection, genotyping and forensic software applications (e.g. Applied Biosystems SeqScape, Paracel Genome Assembler, MTexpert, etc.).

VCAKE is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina's Solexa Sequencing data.