2503 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...-t8 reads.fq reads.fq | gzip -1 > reads.paf.gz Then we can assemble miniasm -f reads.fq reads.paf.gz > reads.gfa Convert GFA to FASTA: awk '/^S/{print ">"$2"...2348 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
...a ("dust", bubbles, merged clusters, sequence-heterogeneous clusters, etc). Many of these additional sources may optionally applied. simNGS takes fasta format sequences and a file d...2347 days ago
jobTree based python wrapper to run the genome simulation tool suite Evolver
...and image files. Also included are convenience scripts to: check on a running simulation and see detailed status and logging information; extract fasta sequence files from the leaf...2337 days ago
Mugsy: multiple whole genome alignment tool
...inear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a...2337 days ago
Biological file format tutorial
...users to distinguish the difference between different formats. Please refer user manual or other information resources on web for more details. FASTA FASTQ SAM BAM VCF GFF G...2328 days ago
xmatchview: smith-waterman alignment visualization
xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and di...2317 days ago
Seal: SEquence ALignment evaluation suite
...ovides several utilities that can be used to evaluate alignment algorithms, including: Reading a pre-existing reference genome from one or more FASTA files. Alternatively, genera...2311 days ago
Jabba: Hybrid Error Correction for Long Sequencing Reads
...ijn graph and a set of sequences: the de Bruijn graph should appear in fasta format with 1 entry per node,...tion should be in the format:>NODE the set of sequences should be in fasta or fastq format. These sequen...1979 days ago
Carefully opt for human reference genome
Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference gen...1535 days ago