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Software, Code and Documents from Laboratori de Proteòmica CSIC/UAB ( LP-CSIC/UAB: http://proteomica.uab.cat )

Magnolya enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares two next-generation sequencing datasets.

...mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others. General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches a target mitochondrial genome given. 2-searches for all mitochondrial gene features and circularization. 3-stores the best result found. 4-uses the best assembly as backbone for a reference based assembly, using MIRA and MITObim, trying to extend the mitogenome and close gaps. 5-annotates the best assembly, identifying the start and end position of each and every feature. 6-creates a folder with all the results (PNG, GENBANK, FASTA, SEQUIN, CAF, MAF and a stats logfile).

MAXIMUS is a genome assembly pipeline which takes the best out of multiple reference assemblies and de novo assembly. The benefits of this approach include better assembled repetitive regions, less gaps and higher accuracy for the resultant assembly.

MetaPepSeq is metaserver for protein identification in Mass Spectrometry Experiments. It helps joining the power of Mascot and de novo sequencing algorithms by merging together into one tool.