Rahul Nayak
A Bioinformatician
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mrFAST: Micro Read Fast Alignment Search Tool
By Neel 3819 days agomrfast.sourceforge.net - mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold,...cutadapt
By Radha Agarkar 3802 days agocutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the...Stampy
By Abhi 3795 days agowww.well.ox.ac.uk - Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of...SpeedSeq
By Jit 3550 days agogithub.com - A flexible framework for rapid genome analysis and interpretation C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth...Mapping NGS
By Abhimanyu Singh 3448 days agowiki.bits.vib.be - NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...To know that you have to align the sequences to the reference sequence. The reference sequence is in most cases...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 3061 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...The "Ifs" and "Buts" of NGS Quality Control and Trimming
By BioStar 646 days agoNGS quality control and trimming are essential steps to ensure reliable and accurate data for analysis. While the "ifs" highlight the clear benefits of these steps, the "buts" remind us of the potential pitfalls. By adopting best practices and...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2973 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
By Seema Singh 3085 days agogithub.com - 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...Genome assembly forensics: finding the elusive mis-assembly
By Jit 2814 days agoamos.sourceforge.net - We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...
