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Ray assembler Ray is a parallel de novo genome assembler that utilises the message-passing interface everywhere and is implemented using peer-to-peer communication. Ray is implemented using the Ray Platform, a message-passing-interface programming framework. Ray is documented in ... [More] Documentation/ (many files) MANUAL_PAGE.txt (command-line options, same as Ray -help) README.md (general) INSTALL.txt (quick installation) Solutions (all bundled in a single Product called Ray) de novo genome assembly (original Ray Technology, re-branded to géno-Ray Technology) quantification of contig abundance (con-Ray Technology) de novo transcriptome assembly (trans-Ray Technology) quantification of transcript expression (express-Ray Technology) de novo meta-genome assembly (méta-Ray Technology) quantificati [Less]

SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. ... [More] Additional applications include OTU-picking and taxonomy assignation available through QIIME v1.9+ SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user. Optionally, it can provide high quality local alignments of rRNA reads against the rRNA database. SortMeRNA works with Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. [Less]