BOL: Related items

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

BioJoker — Tue, 27 Nov 2018 04:43:57 -0600

lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

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

Google Colab : Google Colab is a free cloud service and now it supports free GPU!

Jit — Fri, 31 Jan 2020 01:31:23 -0600

You can: improve your Python programming language coding skills. develop deep learning applications using popular libraries such as Keras, TensorFlow, PyTorch, and OpenCV.

If you have just a single notebook to submit, use the website https://google-colab.com/, it is really easy, on the top right corner click 'submit +'. The earlier you post the more visibility you will get over time

Address of the bookmark: http://colab.research.google.com

Alignment of closely related whole genomes/scaffolds

Rahul Nayak — Fri, 29 Jan 2016 10:37:27 -0600

With the relative ease and low cost of current generation sequencing technologies has led to a dramatic increase in the number of sequenced genomes for species across the tree of life. This increasing volume of data requires tools that can quickly compare multiple whole-genome sequences, millions of base pairs in length, to aid in the study of populations, pan-genomes, and genome evolution.This bookmaks have been created to report new tools for whole genome alignments.

Please report new whole genome alignment tools under comment sections.

Address of the bookmark: http://www.cs.utoronto.ca/~brudno/721.full.pdf

Understanding reads mapping and flags !

Jit — Thu, 25 Apr 2019 09:06:20 -0500

Linear Alignment: An alignment of a read to a single reference sequence that may include insertions, deletions, skips and clipping, but may not include direction changes (i.e. one portion of the alignment on forward strand and another portion of alignment on reverse strand).

Chimeric Alignment: An alignment of a read that cannot be represented as a linear alignment. Typically, one of the linear alignments in a chimeric alignment is considered the “representative” alignment, and the others are called “supplementary” and are distinguished by the supplementary alignment flag.

Chimeric reads are indicative of structural variation in DNA-seq and it may indicate the presence of chimeric genes in RNA-seq.

In short, chimeric reads can be split in to two or more parts, each part would be mapped to reference(it’s not hard-clipped), the total length of the mapped part is longger than read length.

Representative alignment: A chimeric alignment that is represented as a set of linear alignments that do not have large overlaps typically has one linear alignment that is considered the representative alignment.

One read can align to multiple positions, we can find one alignmnet position which sequence do not have large overlaps, it called representative alighment, for other alignment positions, we called them supplementary alignment.

It seems that GATK can realignment those representative reads to the correctly position via RealignerTargetCreator and IndelRealigner. (WARNING: I am not quite sure if I understand this correctly. If someone could help me, please leave me a message below, thanks, thanks.)

Supplementary Alignment: A chimeric reads but not a representative reads.

Primary Alignment and Secondary Alignment: A read may map ambiguously to multiple locations, e.g. due to repeats. Only one of the multiple read alignments is considered primary, and this decision may be arbitrary. All other alignments have the secondary alignment flag.

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

BLAST options, setting and defaults

Jit — Mon, 10 Dec 2018 08:29:37 -0600

BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is best used for sequence similarity searching, rather than for motif searching. For searches using a query sequence of fewer than twenty residues, PatMatch is the best choice. Another sequence alignment tool that may yield different results from BLAST, and may be useful for motif searching, is FASTA. To search nonplant datasets, try NCGR BLAST or NCBI BLAST.

A fairly complete on-line guide to BLAST searching can be found at the NCBI BLAST Help Manual. For a theoretical overview of BLAST, see the NCBI BLAST Course. Additional information can be found in the BLAST 2.0 Release Notes

	BLASTN	BLASTP	BLASTX	TBLASTN	TBLASTX	PSIBLAST
Gap opening penalty: cost to open a gap [integer]	default = 5	default = 11 limited values are supported	default = 11 limited values are supported	default = 11 limited values are supported	default = 11 limited values are supported	default = 5
Gap extension penalty: cost to extend a gap [integer]	default = 2	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default	default = 2
Nucleic match: reward for a match in the BLAST portion of run [integer]	default = 1	n/a	n/a	n/a	n/a	default = 1
Nucleic mismatch: penalty for a mismatch in the blast portion of run [integer]	default = -3	n/a	n/a	n/a	n/a	default = -3
Expectation value: (E) [real]	default = 10.0	default = 10.0	default = 10.0	default = 10.0	default = 10.0	default = 10.0
Word size: the size of the initial word that must be matched between the database and the query sequence	default = 11	default = 3	default = 3	default = 3	default = 3	default = 11
Max scores: Number of one-line descriptions (V) [Integer]	default = 25	default = 25	default = 25	default = 25	default = 25	default = 25
Max alignments: number of alignments to show (B) [integer]	default = 15	default = 15	default = 15	default = 15	default = 15	default = 15
Query filter: filter applied to the query sequence	default = DUST	default = SEG	default = SEG	default = SEG	default = SEG	default = DUST
Query genetic code: genetic code to be used in BLASTX translation of the query	n/a	n/a	default = universal	default = universal	default = universal	n/a
Matrix: substitution matrix to be used for amino acid comparisons	no default	default = blosum62	default = blosum62	default = blosum62	default = blosum62	no default

Supported and Suggested Values for Gap Open and Extension in BLASTP, BLASTX, TBLASTN, and TBLASTX

Gaps Open	Gap Extension
10	1
10	2
11	1
8	2
9	2

Address of the bookmark: https://www.arabidopsis.org/Blast/BLASToptions.jsp

bedtools

Jit — Fri, 24 Feb 2017 04:50:44 -0600

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one tointersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

bedtools is developed in the Quinlan laboratory at the University of Utah and benefits from fantastic contributions made by scientists worldwide.

Address of the bookmark: http://bedtools.readthedocs.io/en/latest/index.html

Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Neel — Fri, 07 Feb 2020 07:16:22 -0600

Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types
Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence in targeted regions.
Consed is compatible with Newbler, Cross_match, Phrap, MIRA, Velvet and PCAP output.
Quickly takes the user to each variant site for viewing (also available as an automated report)
Overview of assembly can help detect and fix misassemblies
Editing time reduced by the program's ability to pin-point problem areas
Editing is guided by error probabilities

Address of the bookmark: http://www.phrap.org/consed/consed.html

Structure of Binary files used for storing sequencing data-bam and sff

Rahul Agarwal — Sun, 11 Aug 2013 14:29:49 -0500

Many times bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is that they occupy less space in memory with maximum information content.

Link for those who looking for structure of Bam and sff file:

Bam:

http://samtools.sourceforge.net/SAMv1.pdf (from page 12)

sff file (for Ion torrent and 454 files):

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff

Binary file Editor and Viewer:

http://mh-nexus.de/en/hxd/

karyoploteR: plot whole genomes with arbitrary data

Abhimanyu Singh — Fri, 02 Feb 2018 03:24:28 -0600

karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR is to offer the user an easy way to plot data along the genome to get broad genome-wide view to facilitate the identification of genome wide relations and distributions.

Address of the bookmark: https://bernatgel.github.io/karyoploter_tutorial/