2165 days ago
BEAP: Blast Extension and Assembly Program
...P discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. h...2154 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
...affold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of bo...2153 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
...used for effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT takes 9.5 days to assemble a human genome based on 54x SMRT data...2185 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
...enome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another rem...2173 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...ake # long sequences against a reference genome ./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam # create an index first and then map ./minimap2 -d MT-human.mmi test/MT-human.fa ./minim...2145 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...ion for each long read and uses this to correct errors in these reads. Using datasets from two DNA-seq BAC clones (CH17-157L1 and CH17-227A2), and human brain cerebellum polyA RNA-se...2084 days ago
2068 days ago
Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
...). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolot...2024 days ago
NovoGraph: building whole genome graphs from long-read-based de novo assemblies
...long-read-based de novo sequence assemblies. We then provide a proof of principle by creating a genome graph of seven ethnically-diverse human genomes. https://f10...1997 days ago