SciLifeLab tutorial for bioinformatics analysis !
...d courses (2012-2014) Metagenomics Workshop 2015 November - Uppsala2016 Novemb...ntroduction to Bioinformatics Using NGS Data 2015 February - Uppsala 2015...- Uppsala Introduction to Genome Annotation 2015 April - Uppsala2016 April - U...2273 days ago
MITObim - mitochondrial baiting and iterative mapping
...bsp;Illumina data, but thanks to the versatility of the MIRA assembler, MITObim supports in principle also data from the Iontorrent, 454 and PacBio se...2252 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
...an genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover...2252 days ago
MIX: Combining multiple assemblies from NGS data
...mulative contig length. The Mix algorithm, approach and results were published in BMC bioinformatics : http://www.biomedcentral.com/1471-2105/14/S15/S16.2252 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...e used for effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT takes 9.5 days to assemble a human genome based on 54x SMRT data, which is 40 time...2249 days ago
Digest: In silico restriction digest of complete genomes
...ber of cleavages yielded by commercially available endonucleases in up-to-date sequenced prokaryotic genomes. When the number of fragments is bellow 50, Pulse Field gel Electrophor...2246 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...scaffolding of de novo genome assemblies based on chromatin interactions. Nature Biotechnology 2013 Dec;31(12):1119-25. doi: 10.1038/nbt.272. PubMed PMID: 24185095. http://shendurel...2246 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...hich contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to >1 megabase....14 Dec;24(12):2041-9. doi: 10.1101/gr.178319.114. PubMed PMID: 25327137.2246 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
...e:Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." bioRxiv (2017): 125534.2246 days ago
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