BOL: Related items

PAired-eND Assembler for DNA sequences

Neel — Wed, 06 Apr 2016 05:25:34 -0500

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

More at https://github.com/neufeld/pandaseq

Address of the bookmark: https://github.com/neufeld/pandaseq

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/

SWALO

Jit — Wed, 30 Nov 2016 05:06:05 -0600

SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing.

Download

Git repository of SWALO is at https://github.com/atifrahman/SWALO.

Address of the bookmark: https://atifrahman.github.io/SWALO/

CISA: Contig Integrator for Sequence Assembly

Neel — Thu, 15 Dec 2016 05:42:21 -0600

A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in order to generate the most optimal assembly. However, few efforts have been pursued to take advantage of multiple assemblies to yield an assembly of high accuracy. In this study, we employ various state-of-the-art assemblers to generate different sets of contigs for bacterial genomes. A tool, named CISA, has been developed to integrate the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools. This tool is implemented in Python and requires MUMmer and BLAST+ to be installed on the local machine. The source code of CISA and examples of its use are available at http://sb.nhri.org.tw/CISA/.

Address of the bookmark: http://sb.nhri.org.tw/CISA/en/CISA

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

MyCC: Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

Jit — Fri, 03 Mar 2017 08:34:23 -0600

MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments.

More at http://www.nature.com/articles/srep24175

Address of the bookmark: https://sourceforge.net/projects/sb2nhri/files/MyCC/

SeqMule: Automated human exome/genome variants detection

Abhimanyu Singh — Tue, 07 Mar 2017 10:12:36 -0600

SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its configuration file. SeqMule also has some built-in functions, such as pooling consensus calls from various callers, plotting a Venn diagram showing intersection among different callers, and downloading databases. SeqMule can be used for both Mendelian disease study and cancer genome study.

Address of the bookmark: http://seqmule.openbioinformatics.org/en/latest/

SSPACE

Jit — Fri, 05 May 2017 05:42:15 -0500

SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or matepair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds. Currently we offer this as a command-line tool in Perl. The input data is given by pre-assembled contig sequences (FASTA) and NGS paired-read data (Illumina/454/Solid FASTA or FASTQ). The final scaffolds are provided in FASTA format.

Address of the bookmark: https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE

Bacterial genome assembly !!

Jit — Fri, 05 May 2017 06:11:22 -0500

This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high quality assemblies of bacterial sequence data. The bacterial sample used in this tutorial will be referred to simply as “Species” since it is live data. This data is paired-end data, meaning that there are forward and reverse reads, which we will designate as Sample_R1.fastq and Sample_R2.fastq, respectively.

https://github.com/jennomics/WorkflowPaper/blob/master/Genome%20Assembly%20and%20Annotation.md

Address of the bookmark: http://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/

NCBI Prokaryotic Genome Annotation Pipeline

Jit — Tue, 16 May 2017 08:56:03 -0500

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume. You can find a more detailed description of the new version of the pipeline in NCBI Handbook chapter. NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/