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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...Hercules: a profile HMM-based hybrid error correction algorithm for long reads
By Jit 2286 days agogithub.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2269 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
By Rahul Nayak 2226 days agosourceforge.net - Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like...ARCS: scaffolding genome drafts with linked reads
By Jit 2167 days agogithub.com - ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 1753 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...KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina...
By Jit 1617 days agogithub.com - KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per...Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
By Jit 1429 days agogithub.com - Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce...Bioinformatics tools for telomere to telomere assembly !
By BioStar 1193 days agooptimize HiFi readsSqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 140 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...
