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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (216 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (673 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (834 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (886 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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TEannot
By Jit 3068 days agourgi.versailles.inra.fr - We advise to run first the TEdenovo pipeline but it is not compulsory. We suppose you begin by running the TEannot pipeline on the example provided in the directory "db/" rather than directly on your own genomic sequences. Thus, from now on, the...RepeatModeler
By Jit 3068 days agowww.repeatmasker.org - RepeatModeler is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat...A5-miseq
By Jit 3068 days agosourceforge.net - _A5-miseq_ is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running _A5-miseq_. Point to note: There are many situations where A5-miseq is not...KisSplice
By Jit 3070 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...OrganellarGenomeDRAW
By Jit 3070 days agoogdraw.mpimp-golm.mpg.de - OrganellarGenomeDRAW is dedicated to convert genetic information stored in GenBank entries to graphical maps. The input text file has to be in GenBank flat file format, whereas the output format can be chosen among several formats. The...Bambus
By Jit 3070 days agowww.cbcb.umd.edu - Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with...EMBOSS Apps
By Jit 3090 days agoemboss.sourceforge.net - The programs are listed in alphabetical order, Look at the individual applications or go to the GROUPS page to search by category. EMBASSY applications are described in separate documentation for each package. Applications in...MEGAN6
By Neel 3092 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...WiseScaffolder
By Poonam Mahapatra 3104 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...Scarpa
By Poonam Mahapatra 3104 days agocompbio.cs.toronto.edu - Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate...
