Latest comments
Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (167 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (624 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (785 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 (837 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
Tag cloud
Bioinformatics, Genome, NGS, assembly, Analysis, tool, reads, Sequencing, Data, alignment, Sequence, Visualization, R, Pipeline, Computational Biology, Genomics, genomes, Annotation, Long, Tools, Tutorial, Software, Fast, Gene, DNA, Plot, sequences, Genomic, Assemblies, PacBio, Package, Assembler, de novo, Synteny, Learn, read, Chromosome, accurate, Interactive, Perl, nanopore, genes, Program, Web, Scaffolding, Database, Server, Python, Mapping, Comparative
Our Sponsors
All site bookmarks
LTR_retriever: accurately identifies and annotates LTR retrotransposons and use LAI to evaluates...
By Neel 2141 days agogithub.com - LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, and/or MGEScan-LTR and generating non-redundant LTR-RT library for genome annotations. By...LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
By Neel 2141 days agogithub.com - LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then...gVolante: Completeness Assessment of Genome/Transcriptome Sequences
By Neel 2141 days agogvolante.riken.jp - A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly...MCAT: Motif Combining and Association Tool
By Neel 2141 days agogithub.com - This is a pipeline for finding motifs in fasta files.It can be run from the command line as follows: usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [-c C][-s S] [-d] [-ff] [-v V]positive_seq negative_seq positional...Gene Ontology Consortium
By Jit 2143 days agowww.geneontology.org - The GO knowledgebase is composed of two primary components: the Gene Ontology (GO), which provides the logical structure of the biological functions (‘terms’) and their relationships to one another, manifested as a directed...Detail annotation of genes !
By Jit 2143 days agoftp.ncbi.nih.gov - gene_info recalculated daily--------------------------------------------------------------------------- tab-delimited one line per GeneID Column header line is the first line in the file. Note: subsets of gene_info are available in the...visNetwork: an R package for network visualization, using vis.js javascript library
By Jit 2145 days agodatastorm-open.github.io - visNetwork is an R package for network visualization, using vis.js javascript library (http://visjs.org/). All remarks and bugs are welcome on github : https://github.com/datastorm-open/visNetwork. Features Based...EyeChrom: Visualizing Chromosome Count Data From Plants
By Jit 2146 days agoeyechrom.com - It's goal is to show chromosmal data per genus. Select the genus, and the plot will show the records found for it in the Chromosome Counts Database. note: Report an issue via Gihub: github.com/roszenil/CCDBcurator and...CroCo: A program to detect potential cross contaminations in HTS assembled transcriptomes using...
By Jit 2146 days agogitlab.mbb.univ-montp2.fr - CroCo is a program to detect cross contamination events in assembled transcriptomes using sequencing reads to determine the true origin of every transcripts.Such cross contaminations can be expected if several RNA-Seq experiments were prepared...kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
By Jit 2147 days ago Comments (1)pachterlab.github.io - kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for...
