Abhimanyu Singh
A bioinformatics beginner
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MeGAMerge: A tool to merge assembled contigs, long reads from metagenomic sequencing runs
By Jit 2901 days agogithub.com - MeGAMerge MeGAMerge (A tool to merge assembled contigs, long reads from metagenomic sequencing runs) Description MeGAMerge is a perl based wrapper/tool that can accept any number of sequence (FASTA) files containing assembled contigs of any...Ensembl comparative genomics resources
By Jitendra Narayan 3195 days agowww.ncbi.nlm.nih.gov - The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny,...BUSCO
By Jitendra Narayan 3216 days agohttp://busco.ezlab.org/ - Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/CrossMap
By Jitendra Narayan 3215 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 (GRCm38)). It supports most commonly...CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
By Jit 3138 days ago Comments (2)github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is...YASS :: genomic similarity search tool
By Jit 3132 days agobioinfo.lifl.fr - YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST,...Nemo – A stochastic, individual-base, genetically explicit simulation platform
By Jit 2979 days agonemo2.sourceforge.net - A recombination map has been added for all multi-locus traits. The map positions (chromosomal) for neutral markers (e.g. SNPs) and loci under selection (QTLs, deleterious mutations, DMIs) can now be specified explicitly, or set at random....Bioinformatics tools and software
By Jit 3068 days agodrive5.com - USEARCH >Extreme high-throughput sequence analysis. Orders of magnitude faster than BLAST. MUSCLE >Multiple sequence alignment. Faster and more accurate than CLUSTALW. UPARSE >OTU clustering for 16S and other marker genes....MEGAN6
By Neel 3048 days ago Comments (1)ab.inf.uni-tuebingen.de - Microbiome analysis using a single application MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application. Taxonomic analysis using the NCBI taxonomy or a customized...Structural variation: the hidden genomic treasure
By Jit 2909 days ago Comments (6)Structural variants (SVs) such as deletions, insertions, duplications, inversions and translocations litter genomes and are often associated with gene expression changes and severe phenotypes (ie. genetic diseases in humans).
