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GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2994 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...Cactus: a reference-free whole-genome multiple alignment program
By Jit 2550 days agogithub.com - Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should...
Software packages for next gen sequence analysis
Last updated 4064 days ago by Rahul Nayak Comments (5)Integrated solutions * CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection,...SATSUMA : Highly sensitive whole-genome synteny alignments.
By Jit 3736 days agosatsuma.sourceforge.net - Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes,...EAGER
By Jit 3524 days agogithub.com - The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process. EAGER encompasses both state-of-the-art tools for each step as well as new complementary tools tailored for ancient DNA data within a single...Sequence - Evolution - Function; Computational Approaches in Comparative Genomics
By Jit 3286 days agowww.ncbi.nlm.nih.gov - Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the...SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files
By Rahul Nayak 1618 days agotelatin.github.io - A general-purpose program to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes functions to interleave and de-interleave FASTQ files, to rename sequences and...SeqCAT: Sequence Conversion and Analysis Toolbox
By Neel 782 days agomtb.bioinf.med.uni-goettingen.de - Your all-in-one solution for smooth conversion of sequence coordinates. Designed for bioinformatics data analysis and daily laboratory work, SeqCAT simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate...CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms
By Jit 3298 days agowebchem.ncbr.muni.cz - Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized...NanoSim: nanopore sequence read simulator based on statistical characterization.
By Jit 3152 days agowww.bcgsc.ca - NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides...
