BOL: All site bookmarks

flo

Jitendra Narayan — Wed, 10 Feb 2016 10:52:32 -0600

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 annotations (maybe manually curated or experimentally verified) are available on the old assembly.

The idea is simple: align the new assembly with the old one (e.g., with BLAT), process the alignment data to define how a coordinate or coordinate range on the old assembly should be transformed to the new assembly (e.g., as a chain file), transform the coordinates (e.g., with liftOver).

https://github.com/wurmlab/flo

Address of the bookmark: https://github.com/wurmlab/flo

Spines

Jitendra Narayan — Tue, 09 Feb 2016 05:07:15 -0600

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, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

http://www.broadinstitute.org/science/programs/genome-biology/spines

Address of the bookmark: http://www.broadinstitute.org/science/programs/genome-biology/spines

Pilon

Rahul Nayak — Mon, 08 Feb 2016 15:56:18 -0600

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 aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

Single base differences
Small indels
Larger indel or block substitution events
Gap filling
Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

CrossMap

Jitendra Narayan — Mon, 08 Feb 2016 15:47:00 -0600

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 used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.

CrossMap is designed to liftover genome coordinates between assemblies. It’s not a program for aligning sequences to reference genome.

We do not recommend using CrossMap to convert genome coordinates between species.

More at http://crossmap.sourceforge.net/

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

liftover

Jitendra Narayan — Mon, 08 Feb 2016 15:45:03 -0600

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

https://www.bioconductor.org/help/workflows/liftOver/

Address of the bookmark: https://github.com/aaronwolen/liftover

n50PlottingTools

Jit — Mon, 08 Feb 2016 15:39:04 -0600

Tools to create plots showing N-statistics for genome assemblies

More at https://github.com/dentearl/n50PlottingTools

Address of the bookmark: https://github.com/dentearl/n50PlottingTools

RATT

Jitendra Narayan — Sun, 07 Feb 2016 16:09:40 -0600

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 strains and even different species, like Plasmodium chabaudi onto P. berghei, between different Leishmania species or Salmonella enterica onto other Salmonella serotypes. RATT is able to transfer any entries present on a reference sequence, such as the systematic id or an annotator's notes; such information would be lost in a de novo annotation.

More at http://ratt.sourceforge.net/

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

BUSCO

Jitendra Narayan — Sun, 07 Feb 2016 16:02:39 -0600

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

More at http://busco.ezlab.org/

Address of the bookmark: http://busco.ezlab.org/

MAKER

Jitendra Narayan — Sun, 07 Feb 2016 15:59:24 -0600

MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.

More at http://www.yandell-lab.org/software/maker.html

Address of the bookmark: http://www.yandell-lab.org/software/maker.html

Recombination detection tool

Jit — Tue, 02 Feb 2016 10:11:14 -0600

A program to detect recombination hotspots using population genetic data.

More at https://github.com/auton1/LDhot

Address of the bookmark: https://github.com/auton1/LDhot