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SISRS: Site Identification from Short Read Sequences
By Abhimanyu Singh 2870 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...ACANA: An accurate and consistent alignment tool for DNA sequences
By Jit 3227 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...S-plot2: creates an interactive, two-dimensional heatmap of sequences
By Jit 2931 days agobitbucket.org - S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
By Jit 2856 days agolbbe.univ-lyon1.fr - The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints. SiLiX adopts a graph-theoretical framework to...Kalign: fast multiple sequence alignment program for biological sequences.
By BioStar 2532 days agogithub.com - Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal format: kalign...IgBLAST 1.17 is now available with improved identification of productive V gene sequences
By Jit 2166 days agoIgBLAST 1.17 is now available with improved identification of productive V gene sequencesdoubletrouble: identify duplicated genes from whole-genome protein sequences and classify
By LEGE 946 days agobioconductor.org - doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal...Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences
By LEGE 402 days agogithub.com - Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2436 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
By Rahul Nayak 1630 days agogithub.com - PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast...
