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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (172 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (628 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (789 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 (841 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Metassembler: merging and optimizing de novo genome assemblies
By Rahul Nayak 2395 days agosourceforge.net - Metassembler combines multiple whole genome de novo assemblies into a combined consensus assembly using the best segments of the individual assemblies. Genome assembly projects typically run multiple algorithms in an attempt to find the single best...EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
By Rahul Nayak 2395 days agoarthropods.eugenes.org - EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University,...HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 2395 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...Scallop: reference-based transcriptome assembler for RNA-seq
By Rahul Nayak 2395 days agogithub.com - Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be...MITObim - mitochondrial baiting and iterative mapping
By Rahul Nayak 2395 days agogithub.com - This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full article can be found here. Kindly cite the article if you are using MITObim in your work. The pipeline was originally developed...The MARVEL assembler
By Jit 2399 days agogithub.com - MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads. The assembly process can be summarized as follows: overlap patch reads overlap...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Jit 2399 days agogithub.com - Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to be error-corrected. After...ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 2403 days agogithub.com - ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper...NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
By Jit 2408 days ago Comments (1)github.com - CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning...D3 javascript for visualization !
By Jit 2410 days agogithub.com - Welcome to the D3 gallery! More examples are available on bl.ocks.org/mbostock. If you want to share an example and don't have your own hosting, consider using Gist and bl.ocks.org. If you want to share or view live examples...
