2095 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
...enerate a core SNP alignment (and ultimately a phylogenomic tree). snippy --cpus 16 --outdir mysnps --ref Listeria.gbk --R1 FDA_R1.fastq.gz --R2 FDA_R2.fastq.gz2022 days ago
wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
...orrection and then builds the consensus from intermediate assembly output. ./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo prefix ./wtpoa-cns -t 16 -i prefix.ctg.lay.gz -fo prefix.ctg.fa1914 days ago
DISTRUCT: a program for the graphical display of population structure
...: 137-138 (2004)] To use the UNIX versions, unzip and untar the files in an appropriate directory using gunzip filename.tar.gz; tar xvf filename.tar where "filename.tar.gz" is the downloaded file. Winz...1865 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
...red stream of BAM alignments. More at https://github.com/ekg/glia glia -f ~/human_g1k_v37.fasta -t 20:62900077-62902077 -v variants.vcf.gz \ -s AAATGTAAACATTTTATA...1556 days ago
pggb: the pangenome graph builder
This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that...1326 days ago
1204 days ago
Public Databases for Bioinformatics !
....edu *NOT BACKED UP* Some parallel programming patterns: # gzip a bunch of files parallel gzip -- *.FILESTOGZIP # fork...tained from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz For use case 3...1136 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), a...846 days ago
SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files
...am to manipulate and parse information from FASTA/FASTQ files, supporting gzipped input files. Includes fu...am delivering high performance analyses Supports FASTA/FASTQ files, also Gzip compressed A growing colle...793 days ago