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- Jit@jit.aber
Jit bookmarked Centurion 3211 days ago

Although centromeres are essential for life and are the subject of extensive research, centromere locations in yeast genomes are difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation assay Hi-C has been...

http://cbio.ensmp.fr/centurion/
- Jit@jit.aber
Jit bookmarked NCBI Remap 3211 days ago

NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use...

http://www.ncbi.nlm.nih.gov/genome/tools/remap
- Thangapandi@Thangapandi
Thangapandi is now a friend with Jit 3212 days ago
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Jit@jit.aber
- Jit@jit.aber
Jit is now a friend with Thangapandi 3212 days ago
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- Jitendra Narayan@admin
Jitendra Narayan bookmarked flo 3212 days ago

flo - same species annotations lift over pipeline Lift over is the process of transferring annotations from one genome assembly to another. Usually lift over is done because there is a new, improved genome assembly for the species and good quality...

https://github.com/wurmlab/flo
- Jitendra Narayan@admin
Jitendra Narayan posted to the wire 3213 days ago

Open software for biologists: from famine to feast http://www.nature.com/nbt/journal/v24/n7/full/nbt0706-801.html #BioLinux #OS
- Jitendra Narayan@admin
Jitendra Narayan bookmarked Spines 3214 days ago

Spines Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments,...

http://www.broadinstitute.org/science/programs/genome-biology/spines
- Jit@jit.aber
Jit posted a new ad in the Opportunity Project Fellow Bioinformatics at Central University of Himachal Pradesh 3214 days ago
- Jit@jit.aber
Jit posted a new ad in the Opportunity RA at Central University of Rajasthan 3214 days ago
- Rahul Nayak@rahul
Rahul Nayak bookmarked Pilon 3214 days ago

Pilon is a software tool which can be used to: Automatically improve draft assemblies Find variation among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads...

https://github.com/broadinstitute/pilon/wiki
- Rahul Nayak@rahul
Rahul Nayak commented on a bookmark liftover 3214 days ago

This tool converts genome coordinates and genome annotation files between assemblies. The input data can be pasted into the text box, or uploaded from a file. If a pair of assemblies cannot be selected from the pull-down menus,...
- Rahul Nayak@rahul
Rahul Nayak posted to the wire 3214 days ago

#Scaffolder #evaluation with #Python #scripts https://github.com/martinghunt/Scaffolder-evaluation/tree/master/Analysis-scripts
- Jitendra Narayan@admin
Jitendra Narayan bookmarked CrossMap 3214 days ago

CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly...

http://crossmap.sourceforge.net/
- Jitendra Narayan@admin
Jitendra Narayan bookmarked liftover 3214 days ago

Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly. More at...

https://github.com/aaronwolen/liftover
Comments
- Rahul Nayak@rahul
  
  Rahul Nayak 3214 days ago
  This tool converts genome coordinates and genome annotation files between assemblies. The input data can be pasted into the text box, or uploaded from a file. If a pair of assemblies cannot be selected from the pull-down menus, a direct lift between them is unavailable.
  https://genome.ucsc.edu/cgi-bin/hgLiftOver
- Jit@jit.aber
Jit bookmarked n50PlottingTools 3214 days ago

Tools to create plots showing N-statistics for genome assemblies More at https://github.com/dentearl/n50PlottingTools

https://github.com/dentearl/n50PlottingTools
- Jit@jit.aber
Jit posted to the wire 3214 days ago

Print all the values between 15 to 17. perl -ne 'print if 15 .. 17' file #Perl #PerlTrick #Range
- Jit@jit.aber
Jit posted to the wire 3214 days ago

Print all the values beetween a pattern "abc" > awk '/abc/{flag=1;next}/mno/{flag=0}flag' file #awk #print #range #pattern
- Rahul Nayak@rahul
Rahul Nayak commented on an answer to a question 3215 days ago

Thanks for your question Kritika. Do you mean Bioconductor ?
- Jitendra Narayan@admin
Jitendra Narayan bookmarked RATT 3215 days ago

RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome. It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between...

http://ratt.sourceforge.net/
- Jitendra Narayan@admin
Jitendra Narayan bookmarked BUSCO 3215 days ago

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs More at http://busco.ezlab.org/

http://busco.ezlab.org/

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