BOL: Related items

ngs-bits - Short-read sequencing tools

Neel — Thu, 16 Jan 2020 23:14:00 -0600

Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:

Binaries for Linux/macOS
From sources for Linux/macOS
From sources for Windows

Address of the bookmark: https://github.com/imgag/ngs-bits

Understanding your reads and mapping !

Neel — Wed, 29 Jan 2020 06:29:55 -0600

One of the best tutorial for beginners ...

https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Address of the bookmark: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Postdoctoral Researcher in Cancer Systems Biology

Mon, 12 Jan 2015 01:44:11 -0600

Postdoctoral Researcher in Cancer Systems Biology
Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford
Grade 7: £30,434 - £37,394 with a discretionary range to £40,847 p.a.
Applications are invited for a Postdoctoral Researcher in Cancer Systems Biology to join a rapidly developing Bioinformatics Research Core group headed by Dr Anastasia Samsonova. The purpose of the role is to develop and deliver integrative approaches to dissect the complexity of cancer as a genomic disease. The research will focus on development and application of effective strategies for mining and integration of complex human *omics datasets and clinical/phenotypic data in cancer studies.

The role sits at the critical interface between genetics and cancer systems biology, and would suit a candidate who is interested in developing a career at the confluence of Statistics/Data Mining/Machine Learning and Biology. Ideally, you will have experience in development of analytical approaches to high-throughput and multivariate data mining and integration gained through a PhD (or equivalent) in a quantitative subject (eg mathematics, statistics, physics, engineering or computer science).

Experience of statistics and/or machine learning techniques is highly desirable as is evidence of prior experience of developing bioinformatics software and/or analysing complex *omics data sets. You will be able to work as part of a team and independently and deliver results to the required standard and schedule. You should be able to organise and prioritise your own work, as well as have excellent communication skills, both written and oral. The post will involve interactions with collaborators from such diverse fields as applied mathematics, statistics, computer science and medicine.

This is a full-time post, fixed-term until 31 March 2017. For informal enquiries, contact Dr Anastasia Samsonova (bioinformatics@oncology.ox.ac.uk).

All applicants must complete a short application form and upload a CV and supporting statement.

The closing date for applications is 12.00 noon on 26 January 2015.

More at https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.display_form

INC-Seq: accurate single molecule reads using nanopore sequencing

Jit — Mon, 27 Nov 2017 10:38:56 -0600

INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.

Address of the bookmark: https://github.com/CSB5/INC-Seq

ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.

Seema Singh — Mon, 30 Apr 2018 04:38:40 -0500

ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.

Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8

Address of the bookmark: https://github.com/VicugnaPacos/ALPACA

Frequent Paired-end reads (PE 2x100) mapping command lines

Jit — Tue, 15 May 2018 08:59:29 -0500

bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam

bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \
&& bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq > r12.bwa.sam

bwa bwasw ../index/bwa/hs37m.fa r12.fq > r12.bwasw.sam

gsnap -A sam -d hs37m r1.fq r2.fq > r12.gsnap.sam

novoalign -r Random -o SAM -f r1.fq r2.fq -i 500 50 -d hs37m-k14s3.novo > r12.novo.sam

smalt map -f samsoft -i 650 -o r12.smalt-k20s13.sam hs37m-k20s13 r1.fq r2.fq

stampy.py -g hs37m -h hs37m -o r12.stampy.sam -M r1.fq,r2.fq

soap -D hs37m.fa.index -a r1.fq -b r2.fq -l 32 -g 3 -u dummy -2 dummy -o r12.soap

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

Jit — Tue, 12 Jun 2018 08:14:41 -0500

P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs.

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/

P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads

BioStar — Fri, 07 Sep 2018 05:19:06 -0500

P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides another practical alternative to existing mate-pair_based approaches or other Protein-based approaches (for instance, PEP_scaffolder ) for scaffolding genome sequences. The most important feature of this method is to improve the completeness of gene regions and long-coding gene regions (for instance, circRNA).

Address of the bookmark: http://www.fishbrowser.org/software/P_RNA_scaffolder/#

Flye: Fast and accurate de novo assembler for single molecule sequencing reads

Rahul Nayak — Sat, 06 Jul 2019 03:48:22 -0500

Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

Address of the bookmark: https://github.com/fenderglass/Flye

Biological databases !

BioStar — Wed, 12 Feb 2020 01:16:29 -0600

Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/