BOL: Related items

GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads

Jit — Mon, 14 May 2018 05:25:48 -0500

This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this documentation, is distributed free of charge. If you use this program in a publication, please cite the following reference:
Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." bioRxiv (2017): 125534.

Address of the bookmark: https://github.com/Reedwarbler/GAPPadder

Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map

Jit — Wed, 11 Mar 2020 01:12:06 -0500

A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)

Link to working demo: https://vgteam.github.io/sequenceTubeMap/

Address of the bookmark: https://github.com/vgteam/sequenceTubeMap

SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files

Rahul Nayak — Tue, 01 Mar 2022 03:13:33 -0600

A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and to count and print statistics on sequence lengths. SeqFu is available for Linux and MacOS.

A compiled program delivering high performance analyses
Supports FASTA/FASTQ files, also Gzip compressed
A growing collection of handy utilities, also for quick inspection of the datasets

Can be easily installed via conda:

conda install -c bioconda seqfu

Address of the bookmark: https://telatin.github.io/seqfu2/

SeqCAT: Sequence Conversion and Analysis Toolbox

Neel — Fri, 14 Jun 2024 14:36:53 -0500

Your all-in-one solution for smooth conversion of sequence coordinates.

Designed for bioinformatics data analysis and daily laboratory work, SeqCAT simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate sequences, and easily validate complex genetic events such as fusions with SeqCAT.

More at https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae422/7683049?login=false

Address of the bookmark: https://mtb.bioinf.med.uni-goettingen.de/SeqCAT/home

CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms

Jit — Tue, 25 Jul 2017 05:03:10 -0500

Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized the field of bioinformatics, and is currently implemented in all free and commercial bioinformatics packages. However, with the advent of Next Generation Sequencing (NGS) and the development of new sequencing techniques, the utility of traditional BLAST implementations is limited. CrocoBLAST combines the accuracy and general applicability of BLAST with computational efficiency, accessibility, and user experience, so that NGS data can be analyzed efficiently even when only modest computational resources are available.

https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST

Address of the bookmark: https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST

Scripts for the analysis of HGT in genome sequence data.

Jit — Wed, 29 Nov 2017 16:44:10 -0600

Scripts for the analysis of HGT in genome sequence data

Address of the bookmark: https://github.com/reubwn/hgt

Many-to-many pairwise alignments of two sequence sets

Poonam Mahapatra — Tue, 19 Jun 2018 08:34:15 -0500

needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. The algorithm uses a dynamic programming method to ensure the alignment is optimum, by exploring all possible alignments and choosing the best. A scoring matrix is read that contains values for every possible residue or nucleotide match. Needleall finds the alignment with the maximum possible score where the score of an alignment is equal to the sum of the matches taken from the scoring matrix, minus penalties arising from opening and extending gaps in the aligned sequences. The substitution matrix and gap opening and extension penalties are user-specified.

Address of the bookmark: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/needleall.html

SDA: Long-read sequence and assembly of segmental duplications

Jit — Tue, 05 Mar 2019 10:00:57 -0600

Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs.

https://github.com/mvollger/SDA

Address of the bookmark: https://www.nature.com/articles/s41592-018-0236-3

Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences

Poonam Mahapatra — Mon, 26 Aug 2019 17:55:24 -0500

Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological sequence analyses but it is limited by the verbosity of traditional alignment presentation styles. Miropeats enhances the utility of conventional DNA sequence comparisons when looking at long lengths of sequence similarity by summarizing extensive large scale sequence similarities on a single page of graphics. The latest version of Miropeats can be used as a general pairwise alignment program or in its traditional role sorting out a big mess of overlapping or similar regions.

Address of the bookmark: http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/

GfaViz: flexible and interactive visualization of GFA sequence graphs

Jit — Thu, 23 Jan 2020 07:33:46 -0600

GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general, and able to represent many different types of sequence graphs, including scaffolding graphs, alignment graphs, variant graphs and splicing graphs.

Address of the bookmark: https://github.com/ggonnella/gfaviz