BOL: Related items

Standardized velvet assembly report

Poonam Mahapatra — Fri, 09 Dec 2016 03:59:59 -0600

Requirements:

velvet (velveth velvetg should be in your PATH)
R (with Sweave)
pdflatex (usually part of TeTeX)
ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable"))
Perl

Optional:

BLAT or BLAST (to generate alignments against a reference genome). If using BLAT, add faToTwoBit,gfClient,gfServer to your PATH. If using BLAST, add blastall and formatdb.

Edit permute.sh to your liking, paying particular attention to the kmer, cvCut, expCov, and other flags

To Run:

perl fastaAllSize mysequences.fa > mysequences.stat or gunzip -c mysequences.fa.gz | fastaAllSize > mysequences.stat Substitute fastqAllSize for fastq files.
./permute.sh mysequences (leave out the .fa)

https://github.com/leipzig/standardized-velvet-assembly-report

Address of the bookmark: https://github.com/leipzig/standardized-velvet-assembly-report

EAGER

Jit — Sat, 10 Dec 2016 18:07:23 -0600

The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.

EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single integrated solution in an easily accessible format.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0918-z

Address of the bookmark: https://github.com/apeltzer/EAGER-GUI

BIMA V3: an aligner customized for mate pair library sequencing

Abhimanyu Singh — Wed, 14 Dec 2016 15:20:00 -0600

Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a challenging and
time consuming process for most NGS alignment programs. Large insert sizes, introduction of library preparation protocol artifacts (biotin junction reads, paired-end read contamination, chimeras, etc.), and presence of structural variant breakpoints within reads increases mapping and alignment complexity. We describe an algorithm that is up to 20 times faster and 25% more accurate than popular NGS alignment programs when processing mate pair sequencing.
Availability: http://bioinformaticstools.mayo.edu/research/bima/
Contact: vasmatzis.george@mayo.edu

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2014/02/12/bioinformatics.btu078.full.pdf

GARM:Genome Assembly, Reconciliation and Merging

Jit — Mon, 19 Dec 2016 06:03:02 -0600

The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux distributions. The method merges contigs or scaffolds from different assemblers using the same or different sequencing technologies. When scaffolds are provided, a process of finding probable compressions or extensions (CE) problems in the assemblies can be per-formed; contigs are joined back into scaffolds after gap recalculation

Address of the bookmark: http://garm-meta-assem.sourceforge.net/

quickmerge: A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.

Jit — Mon, 19 Dec 2016 10:23:36 -0600

quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences, often with dramatic outcomes. The program uses information from assemblies made with illumina short reads and PacBio long reads to improve contiguities of an assembly generated with PacBio long reads alone. This is counterintuitive because illumina short reads are not typically considered to cover genomic regions which PacBio long reads cannot. Although we have not evaluated this program for assemblies generated with Oxford nanopore sequences, the program should work with ONP-assemblies too.

Address of the bookmark: https://github.com/mahulchak/quickmerge