<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44555?offset=120 https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis Wed, 18 Aug 2021 00:02:54 -0500 https://bioinformaticsonline.com/bookmarks/view/43268/kmer-a-suite-of-tools-for-dna-sequence-analysis <![CDATA[Kmer: a suite of tools for DNA sequence analysis]]> More at https://help.rc.ufl.edu/doc/Kmer

This also includes:

  • A2Amapper: ATAC, Assembly to Assembly Comparision tool:
    • Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).
  • Sim4db:
    • Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.
  • LEAFF:
    • LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.
  • Meryl:
    • An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/44481/unialigner-a-parameter-free-framework-for-fast-sequence-alignment Fri, 08 Mar 2024 23:36:12 -0600 https://bioinformaticsonline.com/bookmarks/view/44481/unialigner-a-parameter-free-framework-for-fast-sequence-alignment <![CDATA[UniAligner: a parameter-free framework for fast sequence alignment]]> UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches, such as the Smith-Waterman algorithm, that work well for most sequences, fail to construct biologically adequate alignments of extra-long tandem repeats (ETRs), such as human centromeres and immunoglobulin loci. This limitation was overlooked in the previous studies since the sequences of the centromeres and other ETRs across multiple genomes only became available recently.

More at https://www.nature.com/articles/s41592-023-01970-4

Address of the bookmark: https://github.com/seryrzu/unialigner

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/39104/hipstr-haplotype-inference-and-phasing-for-short-tandem-repeats Thu, 07 Mar 2019 21:13:06 -0600 https://bioinformaticsonline.com/bookmarks/view/39104/hipstr-haplotype-inference-and-phasing-for-short-tandem-repeats <![CDATA[HipSTR: Haplotype inference and phasing for Short Tandem Repeats]]> HipSTR was specifically developed to deal with these errors in the hopes of obtaining more robust STR genotypes. In particular, it accomplishes this by:

  1. Learning locus-specific PCR stutter models using an EM algorithm
  2. Mining candidate STR alleles from population-scale sequencing data
  3. Employing a specialized hidden Markov model to align reads to candidate alleles while accounting for STR artifacts
  4. Utilizing phased SNP haplotypes to genotype and phase STRs

Address of the bookmark: https://github.com/tfwillems/HipSTR

]]> BioJoker https://bioinformaticsonline.com/bookmarks/view/44559/metagraph-ultra-scalable-framework-for-dna-search-alignment-assembly Sat, 08 Jun 2024 16:15:25 -0500 https://bioinformaticsonline.com/bookmarks/view/44559/metagraph-ultra-scalable-framework-for-dna-search-alignment-assembly <![CDATA[MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly]]> The MetaGraph framework is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle, transforming single input samples into error-removed, refined sample graphs, which are then merged into a joint metagraph index. Each input sample is annotated in the joint index as a subgraph. This graph index enriched with metadata can then be used for downstream applications such as sequence search or differential assembly.

Searcg link https://metagraph.ethz.ch/search 

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4 

Address of the bookmark: https://metagraph.ethz.ch/

]]> Abhi