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- Jit@jit.aber
Jit bookmarked BETSY: A new backward-chaining expert system for automated development of pipelines in... 2216 days ago

The BETSY provides a command-line interface and available at https://github.com/jefftc/changlab. A user first searches in the knowledge base for desired output and then BETSY develops an initial workflow to produce that data which is later...

https://github.com/jefftc/changlab
- Jit@jit.aber
Jit posted to the wire 2216 days ago

https://iisc.ac.in/post-docs/ IISc PostDoc #postdoc #iisc
- Jit@jit.aber
Jit posted to the wire 2216 days ago

Bioinformatics training http://ce3c.ciencias.ulisboa.pt/training/?cat=13 #Training
- Jit@jit.aber
Jit bookmarked ARCS: scaffolding genome drafts with linked reads 2216 days ago

ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to...

https://github.com/bcgsc/ARCS/
- Jit@jit.aber
Jit posted to the wire 2216 days ago

https://dl.winehq.org/wine-builds/macosx/download.html #wine #download
- Rahul Nayak@rahul
Rahul Nayak bookmarked Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies 2217 days ago

Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...

https://bitbucket.org/mroachawri/purge_haplotigs
- Jit@jit.aber
Jit bookmarked gpsrdocker: docker-based container that contain all software/web servers developed in the field of... 2217 days ago

GPSRdocker (http://webs.iiitd.edu.in/gpsrdocker/) is Presently it contain software developed at G. P. S. Raghava's group (http://webs.iiitd.edu.in/raghava/ ). The programs and the package are free software for academic users. Permission...

https://hub.docker.com/r/raghavagps/gpsrdocker/
- BioStar@biostar
BioStar posted to the wire 2217 days ago

print_fs("~/flowchart/", depth = 4) #Print #FileStructure
- BioJoker@biojoker
BioJoker posted to the wire 2219 days ago

Victorian Bioinformatics Consortium http://www.vicbioinformatics.com/software.shtml #Bioinformatics #Tools
- BioJoker@biojoker
BioJoker posted a new ad in the Opportunity SERB Sponsored School in Evolutionary Biology 2019, 12–26 March 2019 2219 days ago
- Rahul Nayak@rahul
Rahul Nayak bookmarked EGAD: Ultra-fast functional analysis of gene networks 2220 days ago

With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficient tools to calculate functional properties in networks based on the guilt-by-association principle. These allow rapid controlled...

https://github.com/sarbal/EGAD
- Rahul Nayak@rahul
Rahul Nayak posted to the wire 2220 days ago

sudo find /tmp -type f -atime +10 -delete #Delete all tmp files created within 10 days #Linux
- Rahul Nayak@rahul
Rahul Nayak bookmarked PilonGrid: parallel wrapper around the Pilon framework 2220 days ago

The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the...

https://github.com/skoren/PilonGrid
- Rahul Nayak@rahul
Rahul Nayak posted to the wire 2220 days ago

#Search a #genome sequence for secondary #metabolite biosynthetic gene clusters https://antismash.secondarymetabolites.org/#!/start
- Jit@jit.aber
Jit bookmarked SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences 2221 days ago

The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to...

http://lbbe.univ-lyon1.fr/SiLiX?lang=fr
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh bookmarked KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH... 2221 days ago

KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data...

https://www.kegg.jp/blastkoala/
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh bookmarked KEGG Mapper – Reconstruct Pathway 2221 days ago

Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and metagenome annotations. The input data is a single gene list (for a single organism) or multiple gene lists (for multiple organisms) annotated with KEGG Orthology (KO)...

https://www.kegg.jp/kegg/tool/map_pathway.html
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh bookmarked OrthoANI: An improved algorithm and software for calculating average nucleotide identity 2221 days ago

OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to...

https://www.ezbiocloud.net/tools/orthoani
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh bookmarked genoPlotR - plot gene and genome maps project! 2221 days ago

genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files. Features Linear...

http://genoplotr.r-forge.r-project.org/
- Abhimanyu Singh@abhimanyu
Abhimanyu Singh bookmarked Genome sequence-based (sub-)species delineation. 2221 days ago

The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates differences in genomic G+C...

http://ggdc.dsmz.de/

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