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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (638 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1094 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1255 days ago): Sequencing coverage is defined as the average number of reads that covers...
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PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 2833 days agogithub.com - PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct...EAGLER: a scaffolding tool for long reads.
By Jit 2834 days agogithub.com - EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping...“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
By Poonam Mahapatra 2834 days agodoua.prabi.fr - One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies,...MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
By Poonam Mahapatra 2836 days agowww.fish-evol.com - MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the PAML package. In this tutorial I will analyze an easy...GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2836 days agosourceforge.net - GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
By Poonam Mahapatra 2836 days agomolevol.cmima.csic.es - Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its...Ranbow: a haplotype assembler for polyploid genomes
By Jit 2837 days agowww.molgen.mpg.de - Ranbow is a haplotype assembler for polyploid genomes. It has been developed for the haplotype assembly of the hexaploid sweet potato genome, which is highly heterozygous. Ranbow can also be applied to other polyploid genomes. After a first phasing,...BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing...
By Jit 2838 days agogithub.com - BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a...CrossMap: a program for convenient conversion of genome coordinates
By Jit 2838 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...SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
By Surabhi Chaudhary 2839 days agolbbe.univ-lyon1.fr - SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes located on the non recombining part of sex chromosomes). How does SEX-DETector...
