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SATSUMA : Highly sensitive whole-genome synteny alignments.
...., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51. Tutorial at http://evomics...2970 days ago
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
...rrent mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific Bio...2963 days ago
- ...variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or o...
2949 days ago
- ...or the preliminary assembly, which can be visualised, such as Figure 2a from the paper showing TAGC plots/blobplots for Caenorhabditis sp. 5:
2939 days ago
CovCal: Coverage / Read Count Calculator
Coverage / Read Count Calculator Calculate how much sequencing you need to hit a target depth of coverage (or vice versa). Instructions: set the read length/config...2222 days ago
- ...(2012). “clusterProfiler: an R package for comparing biological themes among gene clusters.” OMICS: A Journal of Integrative Biology, 16(5), pp. 284-287.InstallationTo...
2936 days ago
- ...queries. Kaiju is described in Menzel, P. et al. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257 (open access)....
2925 days ago
- ...ly-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted interactions in 5 organisms. Experimental data...
2918 days ago
Bioinformatics tools and software
USEARCH >Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate t...2917 days ago
- _A5-miseq_ is a pipeline for assembling DNA...rough the steps necessary for running _A5-miseq_. Point to note: There are many situations where A5-miseq is not the right tool f...low in all or most reads before 60nt. A5-miseq assumes it is assemblin...
2873 days ago
