BOL: Related items

Juicebox: Visualization and analysis software for Hi-C data

Jit — Fri, 21 Feb 2020 00:33:38 -0600

Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain primarily to usage of command line tools and the Juicebox jar files.

Juicebox can now be used to visualize and interactively (re)assemble genomes. Check out the Juicebox Assembly Tools Module website https://aidenlab.org/assembly for more details on how to use Juicebox for assembly.

GUI at https://aidenlab.org/juicebox/

Address of the bookmark: https://github.com/aidenlab/Juicebox

wgd—simple command line tools for the analysis of ancient whole-genome duplications

LEGE — Thu, 23 Jul 2020 05:49:45 -0500

wgd is a easy to use command-line tool for K_S distribution construction named wgd. The wgd suite provides commonly used K_S and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.

https://academic.oup.com/bioinformatics/article/35/12/2153/5162749

Address of the bookmark: https://github.com/arzwa/wgd

Kmer: a suite of tools for DNA sequence analysis

BioStar — Wed, 18 Aug 2021 00:02:54 -0500

More at https://help.rc.ufl.edu/doc/Kmer

This also includes:

A2Amapper: ATAC, Assembly to Assembly Comparision tool:
- Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).

Sim4db:
- Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.

LEAFF:
- LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.

Meryl:
- An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

Jit — Wed, 29 Jun 2022 03:22:26 -0500

InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0611-3

Address of the bookmark: http://www.interactivenn.net/

pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction

LEGE — Wed, 21 Feb 2024 06:19:41 -0600

ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Address of the bookmark: https://github.com/AusARG/pipesnake

PheWAS: R package is designed to provide an accessible interface to the phenome wide association study

BioStar — Thu, 30 Jul 2020 22:06:37 -0500

The PheWAS R package is designed to provide an accessible interface to the phenome wide association study. For a description of the methods available and some simple examples, please see the package vignette or the R documentation. For installation help, see below. ##Installing the PheWAS Package The PheWAS package can be installed using the devtools package. The following code when executed in R will get you started:

install.packages("devtools")
#It may be necessary to install required as not all package dependencies are installed by devtools:
install.packages(c("dplyr","tidyr","ggplot2","MASS","meta","ggrepel","DT"))
devtools::install_github("PheWAS/PheWAS")
library(PheWAS)

Address of the bookmark: https://github.com/PheWAS/PheWAS

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers

Jit — Mon, 21 Jan 2019 06:50:05 -0600

A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics

Authors: Qiyun Zhu (qiyunzhu@gmail.com), Katharina Dittmar (katharinad@gmail.com)

Affiliation: Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, USA

Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. BMC Genomics. 2014. 15:717.

Usage: Simply execute perl HGTector.pl, or, open GUI.html in a web browser to see a step-by-step wizard.

Download HGTector 0.2.2.

Address of the bookmark: https://github.com/DittmarLab/HGTector

BEDOPS v2.4.26: high-performance genomic feature operations

Jit — Mon, 12 Jun 2017 10:11:01 -0500

BEDOPS v2.4.26 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

The overview section of the BEDOPS v2.4.26 documentation summarizes the toolkit, functionality and performance enhancements. The reference table offers documentation for all applications and scripts.

Address of the bookmark: https://github.com/bedops/bedops

Check Linux server configuration !!

Rahul Nayak — Tue, 06 May 2014 01:10:57 -0500

Bioinformatician uses servers for computational analysis. Sometime we need to check the server details before running our programs or tools. Here I am showing some basic commands using them you can gather the system/server information.

To check what version of Operating System is installed on the server you can use the following commands:-
=================================================================
1.cat /etc/issue
[root@localhost ~]# cat /etc/issue
Red Hat Enterprise Linux Server release 5.5 (Tikanga)
Kernel \r on an \m

2.cat /etc/redhat-release
[root@localhost ~]# cat /etc/redhat-release
Red Hat Enterprise Linux Server release 5.5 (Tikanga)

3.lsb_release -a
[root@localhost ~]# lsb_release -a
LSB Version:    :core-3.1-ia32:core-3.1-noarch:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 5.5 (Tikanga)
Release:        5.5
Codename:       Tikanga

To check whether the operating system is 32 or 64bit:-
================================
# uname -i
[root@localhost ~]# uname -i
i386
(i386 represents that server is having 32bit operating system)

[root@localhost ~]# uname -i
x86_64
(x86_64 represents that server is having 64bit operating system)

To see the processor/CPU information:-
=============================
# cat /proc/cpuinfo
[root@localhost ~] cat /proc/cpuinfo
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 15
model name      : Intel(R) Xeon(R) CPU            5130 @ 2.00GHz
stepping        : 6
cpu MHz         : 1995.087
cache size      : 4096 KB
physical id     : 0
siblings        : 2
core id         : 0
cpu cores       : 2
apicid          : 0
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
fpu             : yes
fpu_exception   : yes
cpuid level     : 10
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm constant_tsc pni monitor ds_cpl vmx tm2 ssse3 cx16 xtpr lahf_lm
bogomips        : 3990.17
(Here processor number 0 indicates that the system is having one process(processor number starts with zero))

To check memory information:-
===========================
# free -m
[root@localhost ~]# free -m
             total       used       free     shared    buffers     cached
Mem:          5066       3513       1552          0        612       2319
-/+ buffers/cache:        582       4484
Swap:         1983          0       1983

# cat /proc/meminfo
[root@localhost ~]# cat /proc/meminfo
MemTotal:      5187752 kB
MemFree:       1639300 kB
Buffers:        627024 kB
Cached:        2374944 kB
SwapCached:          0 kB
Active:        2458788 kB
Inactive:       920964 kB
HighTotal:     4325164 kB
HighFree:      1561936 kB
LowTotal:       862588 kB
LowFree:         77364 kB
SwapTotal:     2031608 kB
SwapFree:      2031608 kB
Dirty:             704 kB
Writeback:           0 kB
AnonPages:      377892 kB
Mapped:          35328 kB
Slab:           153036 kB
PageTables:       6316 kB
NFS_Unstable:        0 kB
Bounce:              0 kB
CommitLimit:   4625484 kB
Committed_AS:   977132 kB
VmallocTotal:   116728 kB
VmallocUsed:      4492 kB
VmallocChunk:   112124 kB
HugePages_Total:     0
HugePages_Free:      0
HugePages_Rsvd:      0
Hugepagesize:     2048 kB

To check the model and serial name of the server:-
=======================================
[root@localhost ~]# dmidecode | egrep -i "product name|Serial number"
Product Name: PowerEdge R710
Serial Number: AB8CDE1


To check the host name:-
=====================
[root@localhost ~]# uname -n
localhost

[root@localhost ~]# hostname
localhost

To check the kernel version:-
========================
[root@localhost ~]# uname -r
2.6.18-238.9.1.el5PAE

Bioinformatician's summer vacation !!!

Jit — Wed, 03 Sep 2014 13:11:50 -0500

Yes, the bioinformatician do spend their summer vacation like this. They spend more time on cheking the JOBS running on various servers.