Surabhi Chaudhary
A Bioinformatician
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LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific...
By Jit 3081 days agowww.cs.helsinki.fi - LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines. Publication: L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de...Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 2572 days agowww.ncbi.nlm.nih.gov - We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
By Jit 2384 days agogithub.com - This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this...ACANA: An accurate and consistent alignment tool for DNA sequences
By Jit 2543 days agowww.niehs.nih.gov - ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts...D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
By Jit 2356 days agodgenies.toulouse.inra.fr - D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap...DMINDA2: an integrated web server for DNA motif identification and analyses
By BioStar 1754 days agobmbl.sdstate.edu - DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses More at http://bmbl.sdstate.edu/DMINDA2/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086085/Biological databases !
By BioStar 1745 days ago Comments (4)ftp.ncbi.nih.gov - 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.htmlSISRS: Site Identification from Short Read Sequences
By Abhimanyu Singh 2186 days agogithub.com - Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads...GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2373 days ago1001genomes.org - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2331 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...
