<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37302?offset=60 https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads Tue, 08 May 2018 04:27:22 -0500 https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads <![CDATA[HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads]]> HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). 

more at https://ccb.jhu.edu/software/hisat2/index.shtml

Address of the bookmark: https://github.com/infphilo/hisat2

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/37473/lsc-a-long-read-error-correction-tool Thu, 02 Aug 2018 07:39:46 -0500 https://bioinformaticsonline.com/bookmarks/view/37473/lsc-a-long-read-error-correction-tool <![CDATA[LSC :a long read error correction tool]]> Getting Started

These simple steps will help you integrate LSC into your transcriptomics analysis pipeline.

  • Read the LSC_requirements for running LSC.
  • Download and set-up the LSC package.
  • Follow the tutorial to see how LSC works on some example data.
  • Read the manual if anything is unclear.
  • You're ready, Happy LSCing!

Latest publication

Kin Fai Au, Jason Underwood, Lawrence Lee and Wing Hung Wong 
Improving PacBio Long Read Accuracy by Short Read Alignment [Manuscript] 
PLoS ONE 2012. 7(10): e46679. doi:10.1371/journal.pone.0046679

Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37650/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads Fri, 07 Sep 2018 05:19:06 -0500 https://bioinformaticsonline.com/bookmarks/view/37650/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads <![CDATA[P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads]]> P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-pair_based approaches or other Protein-based approaches (for instance, PEP_scaffolder ) for scaffolding genome sequences. The most important feature of this method is to improve the completeness of gene regions and long-coding gene regions (for instance, circRNA).

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/#

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/40212/kalign-fast-multiple-sequence-alignment-program-for-biological-sequences Fri, 01 Nov 2019 00:20:41 -0500 https://bioinformaticsonline.com/bookmarks/view/40212/kalign-fast-multiple-sequence-alignment-program-for-biological-sequences <![CDATA[Kalign: fast multiple sequence alignment program for biological sequences.]]> Kalign is a fast multiple sequence alignment program for biological sequences.

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/41592/refka-a-fast-and-efficient-long-read-genome-assembly-approach-for-large-and-complex-genomes Fri, 01 May 2020 03:00:40 -0500 https://bioinformaticsonline.com/bookmarks/view/41592/refka-a-fast-and-efficient-long-read-genome-assembly-approach-for-large-and-complex-genomes <![CDATA[RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes]]> RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel followed by a final bin-stitching step.

 

Address of the bookmark: https://github.com/AppliedBioinformatics/RefKA

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/43439/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite Wed, 06 Oct 2021 07:01:14 -0500 https://bioinformaticsonline.com/bookmarks/view/43439/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite <![CDATA[MMseqs2: ultra fast and sensitive sequence search and clustering suite]]> MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

]]> Abhi 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/44904/termal-a-fast-and-interactive-terminal-based-viewer-for-multiple-sequence-alignments Mon, 22 Sep 2025 23:51:02 -0500 https://bioinformaticsonline.com/bookmarks/view/44904/termal-a-fast-and-interactive-terminal-based-viewer-for-multiple-sequence-alignments <![CDATA[Termal: a fast and interactive terminal-based viewer for multiple sequence alignments]]> termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC) clusters.

https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true

Address of the bookmark: https://github.com/sib-swiss/termal

]]> LEGE https://bioinformaticsonline.com/news/view/44640/new-blast-core-nucleotide-database-core-nt Tue, 13 Aug 2024 07:12:53 -0500 https://bioinformaticsonline.com/news/view/44640/new-blast-core-nucleotide-database-core-nt <![CDATA[New BLAST Core Nucleotide Database (core_nt)]]> The Core Nucleotide Database (core_nt) is now the default nucleotide BLAST database. Core_nt is also available on the command line. You get faster searches & more focused results.

Core_nt contains the same eukaryotic transcript and gene-related sequences as nt. The core_nt database is nt without most eukaryotic chromosome sequences. Most nucleotide BLAST searches with core_nt will be similar to the nt database. However, core_nt is better than nt for accomplishing your most common BLAST search goals, such as identifying gene-related sequences like transcript sequences and complete bacterial chromosomes. This is because, in recent years, nt has acquired more low-relevance, non-annotated, and non-gene content. 

Learn more: https://ncbiinsights.ncbi.nlm.nih.gov/2024/07/18/new-blast-core-nucleotide-database/

]]> LEGE https://bioinformaticsonline.com/file/view/42693/dna-rna-meme Thu, 28 Jan 2021 11:23:14 -0600 https://bioinformaticsonline.com/file/view/42693/dna-rna-meme <![CDATA[DNA RNA MEME]]> Explain the DNA and RNA with picture ...

]]> Neel