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SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Download Git repository of SWALO is at https://github.com/atifrahman/SWALO.2774 days ago
- Useful script for NGS analysis.
2774 days ago
- Bipype is a very useful program, which prepare a lot of types of bioinformatics analyses. There are three input options: amplicons, W...metatranscriptomic data. If amplicons are input data, then bipype does...amplicons types (ITS or 16S). If WGS are chosen, then bipype finds th...
2773 days ago
- Latest announcement on DBT India. Calls Events Projects Jobs
2770 days ago
- Minia is a short-read assembler based on a de Bruijn graph, capable of assembling...human genome on a desktop computer in a day. The output of Minia.... Minia produces results of similar contiguity and accuracy to ot...and line looks like: ./minia -in reads.fa -kmer-size 31 -abundan...
2766 days ago
- SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achiev...esentation of DNA sequence reads. More at https://github.com/jts/s...onal but suggested) the jemalloc memory allocator (http://www.canonw...
2766 days ago
- fqtools is a software suite for fast processing of FASTQ files. Various file manipulations are supported. Se...list of the subcommands available and a brief description of their purpo...le is specified, fqtools will attempt to read data from stdin. In t...
2766 days ago
Standardized velvet assembly report
Requirements: velvet (velveth velvetg should be in your PATH) R (with Sweave) pdflatex (usuall...art of TeTeX) ggplot2 (from R prompt type install.packages("gg...AT, add faToTwoBit,gfClient,gfServer to your PATH. If using BLA... Substitute fastqAllSize for fastq files. ./permute.sh my...2765 days ago
- ...objective of this activity is to help you understand how to run Velvet in general, how to accurately estimate the insert size of a paired-end library...meters of velvet, and the process involved in producing a de novo as...
2765 days ago
- PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is abl...and tandom duplications with the direction of discordant read pair...el Brudno and Yue Jiang, The original PRISM publication can b...
2764 days ago
