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TelomereHunter
By Jit 2955 days agowww.dkfz.de - TelomereHunter is a tool for estimating telomere content from human whole-genome sequencing data. It is designed to take BAM files from a tumor and a matching control sample as input. However, it is also possible to run TelomereHunter with one input...Bioinformatician’s Pocket Reference !!
By RAJESH DETROJA 4290 days agoinfoplatter.wordpress.com - It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special circumstances!) in our own mother-tongue. Today every...YASRA: Reference based assembler
By Abhimanyu Singh 3293 days agogithub.com - YASRA (Yet Another Short Read Assembler) performs comparative assembly of short reads using a reference genome, which can differ substantially from the genome being sequenced. Mapping reads to reference genomes makes use of LASTZ (Harris et al), a...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2801 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...Tigers genome sequenced
By Rahul Agarwal 4554 days agoOnly 4.4 percent DNA difference between Tiger and house catsOpera: An optimal genome scaffolding program
By Jit 3022 days agosourceforge.net - Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from...
SPAdes hybrid genome assembly
Last updated 3022 days ago by Jit Comments (1)When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3013 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...-
Tools for bacterial whole genome annotation
Last updated 3003 days ago by Radha AgarkarRAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation...
