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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (639 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1096 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1257 days ago): Sequencing coverage is defined as the average number of reads that covers...
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jobTree based python wrapper to run the genome simulation tool suite Evolver
By Jit 3013 days agogithub.com - evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation...FOGSAA: Fast Optimal Global Sequence Alignment Algorithm
By Jit 3013 days agowww.isical.ac.in - Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a...Harvest: a suite of core-genome alignment and visualization tools
By Jit 3014 days agoharvest.readthedocs.io - Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome...kraken: A universal genomic coordinate translator for comparative genomics
By Jit 3015 days agogithub.com - If you planning on conducting a study involving dozens of large genomes, then you do not have to run all pairwise synteny alignments .. simply try kraken: A universal genomic coordinate translator for comparative genomicsComparative genomics scripts
By Jit 3015 days agogithub.com - Comparative genomics educational material and papers bookmarks https://github.com/iansealy/coursera-comparinggenomesACANA: An accurate and consistent alignment tool for DNA sequences
By Jit 3016 days agowww.niehs.nih.gov - ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts...Musket: a multistage k-mer spectrum based corrector
By Jit 3016 days agomusket.sourceforge.net - Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3016 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
By Jit 3016 days agonservant.github.io - HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not...Bandage: interactive visualization of de novo genome assemblies
By Shruti Paniwala 3018 days agorrwick.github.io - Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes,...
