Search Results for "genomics"

EggLib has moved to http://mycor.nancy.inra.fr/egglib/ since version 3.0.0.

CARGO is a high-level framework that can semi-automatically generate software systems optimized for the compressed storage of arbitrary types of large genomic data collections. Straightforward applications of CARGO methods to compress FASTQ and SAM format archives require only a few lines of code, produce solutions that match and sometimes outperform specialized format-tailored compressors, and scale well to multi-TB datasets.

With the rise of improved sequencing technologies, genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach with multiple individuals represented and analyzed together. Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n.

...MGEScan-non-LTR is a software for the identification of non-LTR retrotransposons in genomic sequences, following a computational approach inspired by a generalized hidden Markov model (GHMM). References: 1. M. Rho et al., "De novo identification of LTR retrotransposons in eukaryotic genomes", BMC Genomics (2007) 8:90. 2. M. Rho and H. Tang, "MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes", Nucleic Acids Research (2009) 37:21.

These are Python scripts plus C/C++ programs for automating the reference free genomic analysis described in: Kua C-S, Ruan J, Harting J, Ye C-X, Helmus MR, et al. (2012) Reference-Free Comparative Genomics of 174 Chloroplasts. PLoS One 7(11). http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048995 Analytical concept conceived by CHCannon and CSKua. Original script written in Mathematica by CHCannon.

Software for making Clusters of Orthologous Groups (featuring the new EdgeSearch algorithm). Latest ref: Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. Bioinformatics 2010.

Opensource software projects for genetics and genomics from Sage Bionetworks.

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV