Results for "Reads"
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Steps to find palindrome in genomes !
Palindromes are sequences of nucleotides that read the same backward as forward. They can be present in genomes and have various biological functions. Here are some methods for discovering palindromes in genomes: Direct sequence search: One of the simplest ways to discove...Tags: Palindromes, sequences, nucleotides, reads, backward, forward, methods, steps
422 days ago
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project (DToL) https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05385-yTags: MitoHiFi, python, pipeline, mitochondrial, genome, assembly, PacBio, fidelity, reads
241 days ago
- Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeogr...
Tags: Bioinformatics, Computational Biology, Reads, RAD-Seq, NGS
2991 days ago
RACA: Reference-Assisted Chromosome Assembly
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 reads. http://www.ncbi.nlm.nih.gov/pubmed/23307812 http://bioen-comp...Tags: Bioinformatics, NGS, Assembly, Reference, RACA, Reads
2949 days ago
Trimmomatic: A flexible read trimming tool for Illumina NGS data
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 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 ...Tags: Bioinformatics, Trim, NGS, Illumina, Reads, Trimmomatic
2940 days ago
- SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from http://bioinf.spbau...
Tags: Bioinformatics, NGS, Assembly, Assembler, SPAdes, Reads, Illumina
2936 days ago
- Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and integrates read quality, mate pair orientation and inse...
Tags: Bioinformatics, FASTQ, NGS, ALE, Framework, Stats, Reads, Evaluation, Quality, Assembly
2930 days ago
mrFAST: Micro Read Fast Alignment Search Tool
mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes ...Tags: Bioinformatics, FASTQ, Reads, NGS, Mapping, Alignment, Reference
2930 days ago
