A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contigua...2577 days ago
ANGES: reconstructing ANcestral GEnomeS maps
This page contains the software ANGES 1.01, that aims at reconstucting ancestral genome maps from homologous markers in extant related genomes. Download Program,...2571 days ago
2569 days ago
RNAcon: web-server for the prediction and classification of non-coding RNAs
RNAcon is a web-server for the prediction and classification of non-coding RNAs. It uses SVM-based model for the discrimination between coding and ncRNAs and RandomFo...2511 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...ng) but very noisy (i.e. full of errors) We start with an all against all comparison: minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz Then we can assemble...2378 days ago
Delta: a new Web-based 3D genome visualization and analysis platform
...topology/physical structure with extensive genome annotation by juxtaposing the 3D model with diverse genomic assay outputs. https://github.com/zhangzhwlab/delta2355 days ago
mojolicious: a next generation web framework for the Perl programming language.
...SNI, IDNA, HTTP/SOCKS5 proxy, UNIX domain socket, Comet (long polling), Promises/A+, keep-alive, connection pooling, timeout, cookie, multipart and gzip compression support. Built...2331 days ago
Carefully opt for human reference genome
...lm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz There are several othe...1565 days ago
2179 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...sam # use presets (no test data) ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam # PacBio genomic reads ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford...2173 days ago