BOL: Rahul Nayak's bookmarks

VCF Compare !

Rahul Nayak — Wed, 19 Jan 2022 10:30:14 -0600

compare two BWA mapping methods with the online hg18-mapped data

We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/NA18507_GAIIx_100_chr21.bam>, aligned to the b36/hg18 reference genome)

Address of the bookmark: https://wiki.bits.vib.be/index.php/NGS_Exercise.6#compare_aln_.26_mem_results_with_vcf-compare

DEG 5.0: a database of essential genes in both prokaryotes and eukaryotes

Rahul Nayak — Tue, 30 Mar 2021 11:47:29 -0500

Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a key role in the emerging field, synthetic biology.

DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org.

Address of the bookmark: http://www.essentialgene.org/

DEG 5.0: a database of essential genes in both prokaryotes and eukaryotes

Rahul Nayak — Tue, 30 Mar 2021 11:47:28 -0500

DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org.

Address of the bookmark: http://www.essentialgene.org/

AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads

Rahul Nayak — Sun, 14 Mar 2021 09:42:47 -0500

AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.

More at https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/6146772

Address of the bookmark: https://github.com/huangs001/AlignGraph2

Flanker

Rahul Nayak — Sat, 27 Feb 2021 22:04:53 -0600

Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

Address of the bookmark: https://github.com/wtmatlock/flanker

FastProNGS: fast preprocessing of next-generation sequencing reads

Rahul Nayak — Sat, 26 Dec 2020 08:35:21 -0600

FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest.

Address of the bookmark: https://github.com/Megagenomics/FastProNGS

GEO2R: compare two or more groups of Samples

Rahul Nayak — Sun, 20 Dec 2020 11:49:41 -0600

GEO2R to compare two or more groups of Samples in order to identify genes that are differentially expressed across experimental conditions.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/geo/geo2r/

BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks

Rahul Nayak — Sun, 20 Dec 2020 11:43:45 -0600

With BioJupies you can produce in seconds a customized, reusable, and interactive report from your own raw or processed RNA-seq data through a simple user interface

BioJupies now supports user accounts! Sign in from the top right corner of the page for access to unlimited private notebooks, RNA-seq datasets and alignment jobs.

Address of the bookmark: https://amp.pharm.mssm.edu/biojupies/

Caretta – A multiple protein structure alignment and feature extraction suite

Rahul Nayak — Fri, 18 Dec 2020 02:09:44 -0600

Caretta – a multiple protein structure alignment and feature extraction suite

Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments with a higher coverage than current state-of-the-art tools. Caretta is available as a GUI and command-line application and additionally outputs an aligned structure feature matrix for a given set of input structures, which can readily be used in downstream steps for supervised or unsupervised machine learning.

Address of the bookmark: http://www.bioinformatics.nl/caretta/

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Rahul Nayak — Sun, 17 May 2020 10:27:44 -0500

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.

Address of the bookmark: https://github.com/PapenfussLab/gridss