BOL: Related items

PANDASEQ

Shruti Paniwala — Mon, 23 Jan 2017 04:54:32 -0600

PANDASEQ assembles paired-end Illumina reads into sequences, trying to correct for errors and uncalled bases. The assembler reads two files in FASTQ format with quality information. If amplification primers were used (e.g., to isolate a variable region of the 16S gene, or the constant regions around zinc finger binding residues), they can be removed from the sequence during assembly. The final sequence will correct any uncalled bases in the overlapping region using the complementary strand. When mismatches occur in the overlapping region, the base with the better quality score is chosen.
The algorithm is as follows:

1.Find the positions where the forward and reverse primers match best above the threshold and discard the ends of the sequence, including the primer.
2.Pick and overlap to maximise the probability of the forward and reverse reads having come from a single piece of DNA.
3.Identify the masking of the end of the read with the quality score B or # as done by CASAVA and adjust the probabilities in this region.
4.Construct an assembled sequence between the primers and calculate the quality.
5.Check for various constraints, including quality, length, uncalled bases, and user-supplied modules.

http://neufeldserver.uwaterloo.ca/~apmasell/pandaseq_man1.html

Address of the bookmark: http://neufeldserver.uwaterloo.ca/~apmasell/pandaseq_man1.html

EasyBuild

Jit — Fri, 27 Jan 2017 16:00:43 -0600

EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
A full list of supported software packages is available here.

Address of the bookmark: https://hpcugent.github.io/easybuild/

Harvest

Jit — Tue, 31 Jan 2017 10:57:56 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Address of the bookmark: http://harvest.readthedocs.io/en/latest/index.html

Mercator

Jit — Mon, 06 Feb 2017 04:20:36 -0600

Our basic strategy in building homology maps is to use exons that are orthologous in multiple genomes as map "anchors." Given K genomes, the steps in the map construction are as follows:

For each genome, obtain a set of exon annotations. These annotations can be a combination of both exon predictions (e.g. Genscan) and annotations that have been experimentally verified (e.g. RefSeq). Ideally, we would like to have these annotations be as sensitive as possible. Specificity is not a concern, as incorrect annotations are not likely not have significant alignments with other gene annotations.
Compare all exons against all exons in other genomes and record significant alignments between exons. Currently, we use BLAT to do this all-vs-all comparison with alignments being performed in protein space.
Construct a graph with each vertex corresponding to a exon and edges between vertices whose corresponding exons have significant alignments.
Identify cliques in this graph. These cliques are potential anchors to be used in the map.
Starting with the largest cliques (those that have exons in all or most of the genomes), join neighboring (adjacent in genomic coordinates, in each genome) cliques to form runs. Smaller cliques that are inconsistent with runs formed by larger cliques are filtered out. After the smallest cliques have been considered, cliques that are not part of a run are discarded.
The extents of each run in each genome are outputted as orthologous segments. The cliques from each run are used to output the exact genomic coordinates of anchors within each orthologous segment. These anchors can be used by genomic alignment programs (such as MAVID) to do a detailed alignment of each orthologous segment.

https://www.biostat.wisc.edu/~cdewey/mercator/

Address of the bookmark: https://www.biostat.wisc.edu/~cdewey/mercator/

PhD program in Computer Science at University of Essex

Sat, 11 Feb 2017 13:11:36 -0600

As part of the PhD program in Computer Science at University of Essex, I am looking for a PhD student in computational and synthetic biology.
The ideal candidate is interested in designing new biological design automation methods for genome scale projects and/or network modelling of genomic, transcriptomic and proteomic data.
Candidates interested in developing optimization algorithms for biological problems are encouraged to apply as well.
A summary of the research work in the lab can be found on o this page.

Candidates interested in the position should contact me in advance by email to: g.stracquadanio@essex.ac.uk

The deadline for the application is 28/02/2017; info about the application can be found on the Essex CSEE website.

MafTools

Jit — Thu, 16 Feb 2017 11:16:01 -0600

maftools - An R package to summarize, analyze and visualize MAF files. Introduction.

With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widley accepted and used to store variants detected. The Cancer Genome Atlas Project has seqenced over 30 different cancers with sample size of each cancer type being over 200. The resulting data consisting of genetic variants is stored in the form of Mutation Annotation Format. This package attempts to summarize, analyze, annotate and visualize MAF files in an efficient manner either from TCGA sources or any in-house studies as long as the data is in MAF format. Maftools can also handle ICGC Simple Somatic Mutation format.

maftools is on bioRxiv

Please cite the below if you find this tool useful for you.

Mayakonda, A. and H.P. Koeffler, Maftools: Efficient analysis, visualization and summarization of MAF files from large-scale cohort based cancer studies. bioRxiv, 2016. doi: http://dx.doi.org/10.1101/052662

Address of the bookmark: https://github.com/PoisonAlien/maftools

BioDownloader

Surabhi Chaudhary — Sat, 25 Feb 2017 17:52:33 -0600

BioDownloader is a program for downloading and/or updating files from ftp/http servers. The program has unique features that are specifically designed to deal with bioinformatics data files and servers:

optimized to work with vast amount of data and very large file sets (~ 10,000 - 100,000).
allows the selective retrieval of only the required files (file masks, ls-lR parsing, recursive search, updates)
has a built-in repository containing the settings for the most common bioinformatics download needs
built-in wizard for batch post-processing of downloaded files (archive extraction, file conversion, etc.)
capable of performing multiple download or update tasks simultaneously

BioDownloader has a built-in repository containing the settings for common bioinformatics file-synchronization needs, including the Protein Data Bank (PDB) and National Center for Biotechnology Information (NCBI) databases. It can post-process downloaded files, including archive extraction and file conversions.

http://dunbrack.fccc.edu/BioDownloader/

Address of the bookmark: http://dunbrack.fccc.edu/BioDownloader/

DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes

Abhimanyu Singh — Fri, 17 Feb 2017 16:13:35 -0600

The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts for the distance between neighboring genes on each DNA molecule and the BLAST E-value score between homologs, maximally scoring chains of ordered gene pairs are computed and reported. This algorithm can be used to mine large evolutionary conserved regions of genomes between two organisms. Alternatively, by examining colinear sets of homologous genes found within a single genome, segmental genome duplications can be revealed.

This software distribution includes both the DAGchainer utility and a Java-based graphical interface that allows the inputs and outputs to be navigated and interrogated dynamically.

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

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data

Jit — Fri, 24 Feb 2017 04:55:41 -0600

ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, they report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencing data. They also show applicability of the method for variant calling and allele dosage estimation. Results for simulated and real datasets are discussed and provide evidence that ConPADE performs well as long as enough sequencing coverage is available, or the true contig ploidy is low.

https://github.com/microsoftgenomics

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

PBSuite: Software for Long-Read Sequencing Data from PacBio

Jit — Mon, 27 Feb 2017 09:54:47 -0600

PBJelly - the genome upgrading tool.
PBHoney - the structural variation discovery tool

Both are contained within the PBSuite code found in downloads.

----- PBJelly -----
Read The Paper
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0047768

PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes.

----- PBHoney -----
Read The Paper
http://www.biomedcentral.com/1471-2105/15/180/abstract

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

Address of the bookmark: https://sourceforge.net/projects/pb-jelly/