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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (168 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (625 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (786 days ago): Sequencing coverage is defined as the average number of reads that covers...
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Bacterial genome assembly !!
By Jit 2760 days agobioinformatics.uconn.edu - This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high quality assemblies of bacterial sequence data. The bacterial sample used in this tutorial will be...CLA: Contig-Layout-Authenticator
By Jit 2760 days agojournals.plos.org - To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads,...SSPACE
By Jit 2760 days agowww.baseclear.com - SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or...Tetra-Nucleotide Analysis
By Jit 2761 days agochunlab.wordpress.com - A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides in bacterial genomes contain useful, albeit weak, phylogenetic signals. Even though...Fastq format
By Jit 2762 days agoen.wikipedia.org - FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a...Mapping NGS
By Abhimanyu Singh 2763 days agowiki.bits.vib.be - NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...To know that you have to align the sequences to the reference sequence. The reference sequence is in most cases...Enrichr: a comprehensive gene set enrichment analysis
By Jit 2768 days agoamp.pharm.mssm.edu - Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse...DIAMOND
By Jit 2768 days agogithub.com - DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer...DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation...
By Jit 2776 days ago Comments (1)github.com - DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies Our work is published in Scientific Reports: Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous...ChromHMM: Chromatin state discovery and characterization
By Abhimanyu Singh 2776 days agocompbio.mit.edu - ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial...
