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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (332 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (789 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (950 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 (1002 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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DISCOVAR
By Abhimanyu Singh 3306 days agowww.broadinstitute.org - DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or...LASTZ
By Abhi 3306 days ago Comments (2)www.bx.psu.edu - LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as...Trimmomatic: A flexible read trimming tool for Illumina NGS data
By Jit 3309 days agowww.usadellab.org - Paired End: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10...Understanding Fastqc Output
By Jit 3309 days agowww.bioinformatics.babraham.ac.uk - Understanding Following table and graphs Duplication level kmer profile per base GC content per base N content per base quality per base sequence content per sequence GC content per sequence quality sequence length distribution More at...SCALCE
By Surabhi Chaudhary 3309 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 3317 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 3317 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 3317 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 3318 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 3318 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...
