PepNovo is a de novo sequencing algorithm for MS/MS spectra. PepNovo accepts MS/MS spectra in the following formats: dta,mgf,mzxml. This version of PepNovo is optimized for ion-trap mass spectromtetry that uses CID fragmentation (charges 1-3, dominant b/y ladders).
DeNovo Pipeline performes protein identification by de novo interpretation by coupling the PepNovo software for sequencing and the Fasta tool for homology searching.
::DEVELOPER
pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)
CStone is a de novo assembler for RNA-Seq data that uses de Bruijn like graphs and annotates each contig produced with one of three graph classification levels indicating whether or not it can be guaranteed to be non chimeric.
PRICE (Paired-Read Iterative Contig Extension) is a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler.
ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
fq2dna is a command line tool to ease the de novo assembly of archaea, bacteria or virus genomes from raw high-throughput sequencing (HTS) paired-end (PE) reads.
HipMer is a high-performance application that produces high-quality de novo assemblies for very large-scale genomes.
The MetaHipMer extension is a recent addition to HipMer that is geared to large metagenomes and leverages iterative kmer sizes and a specialized scaffolding algorithm to produce increased contiguity and accuracy in metagenomic assemblies. It is able to reconstruct rRNA elements via a separate algorithm which relies on reference SSU and LSU Hidden Markov Models to help traverse the contig graph around ribosomal RNA regions.
E. Georganas et al.,
“HipMer: an extreme-scale de novo genome assembler,”
SC ’15: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2015, pp. 1-11, doi: 10.1145/2807591.2807664.
Hofmeyr S, Egan R, Georganas E, Copeland AC, Riley R, Clum A, Eloe-Fadrosh E, Roux S, Goltsman E, Buluç A, Rokhsar D, Oliker L, Yelick K. Terabase-scale metagenome coassembly with MetaHipMer.
Sci Rep. 2020 Jul 1;10(1):10689. doi: 10.1038/s41598-020-67416-5. PMID: 32612216; PMCID: PMC7329831.