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MAKER
By Jitendra Narayan 3212 days ago Comments (1)www.yandell-lab.org - MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats,...Bpipe - a tool for running and managing bioinformatics pipelines
By Radha Agarkar 3108 days agohttp://docs.bpipe.org/ - Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'. January 20th, 2016 - New! Bpipe 0.9.9 released! Download latest, all Documentation Mailing List (Google...HiCdat
By Jit 3207 days agogithub.com - HiCdat: a fast and easy-to-use Hi-C data analysis tool HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes,...KisSplice
By Jit 3021 days agokissplice.prabi.fr - KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number...Machine Learning !!!
By Gudiya Pal 3067 days agowww.r2d3.us - In machine learning, computers apply statistical learning techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions. Keep scrolling. Using a data set about homes, we will...WiseScaffolder
By Poonam Mahapatra 3055 days agoabims.sb-roscoff.fr - Function WiseScaffolder is a stand-alone semi-automatic application for genome scaffolding of pre-assembled contigs using mate-pair data. It also produces editable scaffold maps, allowing either to build gapped scaffolds or usable as a common...CrossMap
By Abhimanyu Singh 3001 days agocrossmap.sourceforge.net - CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10...LUMPY
By Shruti Paniwala 3012 days agogithub.com - A probabilistic framework for structural variant discovery. Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. 2014. "LUMPY: a Probabilistic Framework for Structural Variant Discovery." Genome Biology 15 (6):...Ka, Ks and Ka/Ks calculations
By Poonam Mahapatra 3008 days agolonglab.uchicago.edu - gKaKs is a codon-based genome-level Ka/Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including...Redundans
By Jit 3005 days agogithub.com - Redundans pipeline assists an assembly of heterozygous genomes.Program takes as input assembled contigs, paired-end and/or mate pairs sequencing libraries and returns scaffolded homozygous genome assembly, that should...
