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The objective of this activity is to help you understand how to run Velvet in general, how to accurately estimate the insert size of a paired-end library through the use of Bowtie, the primary parameters of velvet, and the process...

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...

fqtools is a software suite for fast processing of FASTQ files. Various file manipulations are supported. See below for a full list of the subcommands available and a brief description of their purpose. Most of the individual...

Try this  hierarchical genome assembly (HGA) assembler https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4779561/

SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. More at https://github.com/jts/sga SGA...

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn...

MiraConvert http://manpages.ubuntu.com/manpages/xenial/man1/miraconvert.1.html #MIRA #Assembler #Convert

BLAST cheats heat http://www.vicbioinformatics.com/documents/Quick_Start_Guide_BLAST_to_BLAST+.pdf #BLAST #NCBI #Cheat

The EVE programming language http://witheve.com/ # Programming #Language #EVE

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Bipype is a very useful program, which prepare a lot of types of bioinformatics analyses. There are three input options: amplicons, WGS (whole genome sequences) and metatranscriptomic data. If amplicons are input data, then bipype does...

Useful script for NGS analysis.

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...

Pune University Bioinformatics webpage http://bioinfo.net.in/ #Pune #Bioinformatics

RA Pune University http://bioinfo.net.in/advertisement/ra19-dec-2016.pdf #Pune #RA #India #Job

EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by...