<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38304?offset=10 https://bioinformaticsonline.com/bookmarks/view/42645/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite Mon, 18 Jan 2021 10:47:56 -0600 https://bioinformaticsonline.com/bookmarks/view/42645/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

]]> Manisha Mishra https://bioinformaticsonline.com/bookmarks/view/37457/nanofilt-filtering-and-trimming-of-long-read-sequencing-data Mon, 30 Jul 2018 12:01:52 -0500 https://bioinformaticsonline.com/bookmarks/view/37457/nanofilt-filtering-and-trimming-of-long-read-sequencing-data <![CDATA[nanofilt: Filtering and trimming of long read sequencing data]]> Filtering on quality and/or read length, and optional trimming after passing filters.
Reads from stdin, writes to stdout.

Intended to be used:

  • directly after fastq extraction
  • prior to mapping
  • in a stream between extraction and mapping

https://github.com/wdecoster/nanofilt

Address of the bookmark: https://github.com/wdecoster/nanofilt

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40792/haslr-a-tool-for-rapid-genome-assembly-of-long-sequencing-reads Fri, 31 Jan 2020 05:50:15 -0600 https://bioinformaticsonline.com/bookmarks/view/40792/haslr-a-tool-for-rapid-genome-assembly-of-long-sequencing-reads <![CDATA[HASLR: a tool for rapid genome assembly of long sequencing reads]]> HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation Sequencing reads (such as Illumina) from the same sample. 

Address of the bookmark: https://github.com/vpc-ccg/haslr

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/34493/plast-a-fast-accurate-and-ngs-scalable-bank-to-bank-sequence-similarity-search-tool Fri, 01 Dec 2017 04:10:54 -0600 https://bioinformaticsonline.com/bookmarks/view/34493/plast-a-fast-accurate-and-ngs-scalable-bank-to-bank-sequence-similarity-search-tool <![CDATA[PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool]]> PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

Relying on unique software architecture, PLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

PLAST stands for Parallel Local Sequence Alignment Search Tool and is was published in BMC Bioinformatics.

PLAST is a general purpose sequence comparison tool providing the following benefits:

  • PLAST is a high-performance sequence comparison tool designed to compare two sets of sequences (query vs. reference),
  • Reduces the processing time of sequences comparisons while providing highest quality results,
  • Contains a fully integrated data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.),
  • Does not require any additional hardware, since it is a software solution. It is easy to install, cost-effective, takes full advantage of multi-core processors and uses a small RAM footprint,
  • Ready to be used on desktop computer, cluster, cloud as well as within distributed system running Hadoop.

https://plast.inria.fr/

Address of the bookmark: https://plast.inria.fr/

]]> Jit 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/37643/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads Thu, 06 Sep 2018 16:21:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37643/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads <![CDATA[LoRMA: A tool for correcting sequencing errors in long reads]]> An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are further polished using long-distance dependencies that are found using multiple alignments. According to our experiments, the proposed method is the most accurate one relying on long reads only for read sets with high coverage. Furthermore, when the coverage of the read set is at least 75×, the throughput of the new method is at least 20% higher.

conda install -c atgc-montpellier lorma

Address of the bookmark: https://gite.lirmm.fr/lorma/lorma-releases/wikis/home

]]> Abhimanyu Singh https://bioinformaticsonline.com/blog/view/44616/basics-of-blast-programs Fri, 26 Jul 2024 06:04:26 -0500 https://bioinformaticsonline.com/blog/view/44616/basics-of-blast-programs <![CDATA[Basics of BLAST Programs !]]> The Basic Local Alignment Search Tool (BLAST) is a powerful bioinformatics program used to compare an input sequence (such as DNA, RNA, or protein sequences) against a database of sequences to find regions of similarity. Developed by the National Center for Biotechnology Information (NCBI), BLAST is widely used for identifying species, finding functional and evolutionary relationships between sequences, and predicting the function of novel sequences.

Key Features of BLAST:
1. Sequence Comparison: BLAST searches for local alignments between the query sequence and sequences in a database. It identifies regions of similarity, which can help infer functional and evolutionary relationships.

2. Speed and Efficiency: BLAST uses heuristic algorithms, making it faster than exhaustive search methods, suitable for large-scale database searches.

3. Versatility: There are several versions of BLAST for different types of sequence comparisons:
- blastn: Compares a nucleotide query sequence against a nucleotide sequence database.
- blastp: Compares a protein query sequence against a protein sequence database.
- blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
- tblastn: Compares a protein query sequence against a nucleotide sequence database translated in all reading frames.
- tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

4. Scoring and E-value: BLAST results are scored based on the quality and length of the alignments. The E-value (expect value) indicates the number of alignments one can expect to find by chance, with lower E-values representing more significant matches.

5. Output Formats: BLAST provides results in various formats, including plain text, HTML, XML, and JSON, making it adaptable for different types of analyses and integrations with other tools.

Applications of BLAST:
- Genomic Research: Identifying genes, understanding genetic diversity, and mapping genome sequences.
- Protein Function Prediction: Inferring the function of unknown proteins by comparing them to known protein sequences.
- Evolutionary Studies: Exploring evolutionary relationships between organisms by comparing their genetic material.
- Medical Research: Identifying pathogens, understanding disease mechanisms, and developing treatments by comparing sequences of interest.

Overall, BLAST is an essential tool in bioinformatics, offering a reliable and efficient way to analyze and interpret biological sequence data.

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/40707/vt-a-variant-tool-set-that-discovers-short-variants-from-next-generation-sequencing-data Tue, 28 Jan 2020 03:44:43 -0600 https://bioinformaticsonline.com/bookmarks/view/40707/vt-a-variant-tool-set-that-discovers-short-variants-from-next-generation-sequencing-data <![CDATA[vt: a variant tool set that discovers short variants from Next Generation Sequencing data.]]> vt is a variant tool set that discovers short variants from Next Generation Sequencing data.

https://genome.sph.umich.edu/wiki/Vt

https://github.com/atks/vt

Address of the bookmark: https://genome.sph.umich.edu/wiki/Vt

]]> Jit https://bioinformaticsonline.com/bookmarks/view/36950/salsa-a-tool-to-scaffold-long-read-assemblies-with-hi-c Fri, 15 Jun 2018 04:01:15 -0500 https://bioinformaticsonline.com/bookmarks/view/36950/salsa-a-tool-to-scaffold-long-read-assemblies-with-hi-c <![CDATA[SALSA: A tool to scaffold long read assemblies with Hi-C]]> Address of the bookmark: https://github.com/machinegun/SALSA

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection Wed, 08 May 2024 07:02:55 -0500 https://bioinformaticsonline.com/bookmarks/view/44527/alvis-a-tool-for-contig-and-read-alignment-visualisation-and-chimera-detection <![CDATA[Alvis: a tool for contig and read ALignment VISualisation and chimera detection]]> Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector images. Additionally, Alvis will highlight potentially chimeric reads or contigs, a common source of misassemblies.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04056-0

Address of the bookmark: https://github.com/SR-Martin/alvis

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