Latest comments
Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (638 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1094 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1255 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 (1307 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, Fast, Tools, Software, Tutorial, Gene, Genomic, sequences, DNA, Plot, Assemblies, PacBio, Package, Assembler, de novo, Synteny, accurate, Learn, read, Chromosome, Interactive, Perl, nanopore, genes, Program, Web, Scaffolding, Database, Server, Python, Mapping, Comparative
Our Sponsors
All site bookmarks
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Jit 2809 days ago Comments (1)github.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC...CGView - Circular Genome Viewer
By Rahul Nayak 2818 days agowishart.biology.ualberta.ca - CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature...minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
By Jit 2818 days agogithub.com - git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and then map ./minimap2 -d MT-human.mmi...SWALO: Scaffolding with assembly likelihood optimization
By Jit 2818 days agoatifrahman.github.io - SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to...Many-to-many pairwise alignments of two sequence sets
By Poonam Mahapatra 2819 days agoemboss.sourceforge.net - needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two...mScaffolder: A comparative genome scaffolding tool
By Jit 2823 days agogithub.com - A comparative genome scaffolding tool based on MUMmer mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2823 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference...
By Jit 2824 days agohttp://assemblytics.com/ - Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip...RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
By Neel 2826 days agogithub.com - RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process. It can also analyze multiple genomes...Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from...
By Jit 2826 days agogithub.com - Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by...
