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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (641 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1097 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1258 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 (1311 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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SCALCE
By Surabhi Chaudhary 3617 days agosfu-compbio.github.io - SCALCE (/skeɪlz/, a.k.a. boosting Sequence Compression Algorithms using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any...PhyloGrapher - Graph Visualization Tool
By Jitendra Prajapati 3626 days agowww.atgc.org - PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements).PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In...REAPR: a universal tool for genome assembly evaluation
By Jitendra Prajapati 3626 days ago Comments (1)genomebiology.biomedcentral.com - REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and...QUAST: quality assessment tool for genome assemblies
By Jitendra Prajapati 3626 days ago Comments (2)bioinformatics.oxfordjournals.org - QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.It can works both with and without a given reference genome.The tool accepts multiple assemblies, thus is suitable for comparison. More...PEAR: a fast and accurate Illumina Paired-End reAd mergeR
By Jit 3626 days agowww.exelixis-lab.org - PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the...RACA: Reference-Assisted Chromosome Assembly
By Priya Singh 3626 days ago Comments (1)bioen-compbio.bioen.illinois.edu - Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end...Sequence assembly with MIRA 4
By Priya Singh 3626 days ago Comments (1)mira-assembler.sourceforge.net - MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome and EST/RNASeq projects. MIRA assembles/maps reads gained by electrophoresis sequencing (aka Sanger sequencing) 454 pyro-sequencing (GS20, FLX or Titanium) Ion...PAired-eND Assembler for DNA sequences
By Neel 3626 days agogithub.com - PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. More at https://github.com/neufeld/pandaseqAwesome bioinformatics pipelines !
By Jitendra Prajapati 3633 days agogithub.com - A curated list of awesome pipeline toolkits ... https://github.com/pditommaso/awesome-pipelineRNA-Seq De novo Assembly Using Trinity
By Surabhi Chaudhary 3640 days agogithub.com - Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules:...
