BOL: Related items

PANEV: an R package for a pathway-based network visualization

Jit — Sun, 09 Feb 2020 12:41:52 -0600

PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on information available on KEGG, it visualizes genes within a network of multiple levels (from 1 to n) of interconnected upstream and downstream pathways. The network graph visualization helps to interpret functional profiles of a cluster of genes.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3371-7

Address of the bookmark: https://github.com/vpalombo/PANEV

Proksee: in-depth characterization and visualization of bacterial genomes

LEGE — Tue, 09 May 2023 19:38:52 -0500

Proksee is an expert system for genome assembly, annotation and visualization. To begin using Proksee, provide a complete genome sequence, sequencing reads or a CGView/Proksee map JSON file.

Address of the bookmark: https://proksee.ca/

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

LEGE — Tue, 10 Sep 2024 04:54:55 -0500

NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes

NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of the whole genome or local region and genomic features (e.g. repeats, structural variations, genes) across multiple genomes with a high customization. NGenomeSyn provides an easy way for its users to visualize a large amount of data with a rich layout by simply adjusting options for moving, scaling, and rotation of target genomes. Moreover, NGenomeSyn could be applied on the visualization of relationships on non-genomic data with similar input formats.

https://academic.oup.com/bioinformatics/article/39/3/btad121/7072460

Address of the bookmark: https://github.com/hewm2008/NGenomeSyn

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/

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

BamView: a free interactive display of read alignments in BAM data files

Neel — Fri, 09 Nov 2018 13:43:22 -0600

To run the application on UNIX from the downloaded jar file run the UNIX:

java -mx512m -jar BamView.jar

and extra command line options are given when '-h' is used:

java -jar BamView.jar -h

BAM files can be specified on the command line with the '-a' option:

java -mx512m -jar BamView.jar -a pathToFile/sorted.bam

If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.

Address of the bookmark: http://bamview.sourceforge.net/

pbmm2:A minimap2 frontend for PacBio native data formats

BioStar — Tue, 18 Feb 2020 03:36:22 -0600

pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.

Address of the bookmark: https://github.com/PacificBiosciences/pbmm2

DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution

Jit — Tue, 10 Nov 2020 20:26:00 -0600

The DADA2 tutorial goes through a typical workflow for paired end Illumina Miseq data: raw amplicon sequencing data is processed into the table of exact amplicon sequence variants (ASVs) present in each sample.

The DADA2 Workflow on Big Data goes through workflow optimized to run on large datasets (10s of millions to billions of reads).

An ITS-specific version of the DADA2 workflow identifies and verifiably removes primers on both ends of each ITS read, a key step due to the variable length of the ITS region.

Short demonstrations of assigning taxonomy and assigning species to sequences.

Address of the bookmark: https://benjjneb.github.io/dada2/index.html

PLAR: Pipeline for lncRNA annotation from RNA-seq data

Abhi — Fri, 07 Jan 2022 06:18:01 -0600

Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synteny). One is comparing human GENCODE genes (from GENCODE v30) to lncRNAs from other species identified by PLAR. Available here.

Species	Assembly	Code	Transcriptome	lncRNAs	Protein-coding
Human	hg19	hg19	Download	Download	Download
Rhesus	rheMac3	rm3	Download	Download	Download
Marmoset	calJac3	cj3	Download	Download	Download
Mouse	mm9	mm9	Download	Download	Download
Rabbit	oryCun2	oc2	Download	Download	Download
Dog	canFam3	cf3	Download	Download	Download
Ferret	musFur1	oa3	Download	Download	Download
Opossum	monDom5	md5	Download	Download	Download
Chicken	galGal4	gg4	Download	Download	Download
Lizard	anoCar2	ac2	Download	Download	Download
Coelacanth	latCha1	lc1	Download	Download	Download
Zebrafish	danRer7	dr7	Download	Download	Download
Stickleback	gasAcu1	ga1	Download	Download	Download
Nile tilapia	oreNil2	ot2	Download	Download	Download
Spotted gar	lepOcu1	lo1	Download	Download	Download
Elephant shark	calMil1	cm1	Download	Download	Download
Sea urchin	strPur4	sp4	Download	Download	Download

Address of the bookmark: http://www.weizmann.ac.il/Biological_Regulation/IgorUlitsky/PLAR

gget

BioStar — Sat, 01 Apr 2023 09:42:07 -0500

gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.

Address of the bookmark: https://github.com/pachterlab/gget