From cda0794358c802dc713be17fd7ff0aeafc397e8c Mon Sep 17 00:00:00 2001 From: "Ivan Sovic (T530)" Date: Thu, 12 Nov 2015 18:03:25 +0100 Subject: [PATCH] Updated the README. --- README.md | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 782f32c..4bf0c81 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,18 @@ ## GraphMap - A highly sensitive and accurate mapper for long, error-prone reads **__Current Version: 0.22__** Release date: 12 November 2015 - + Updates: -- Many tiny bug fixes, mostly related to anchored alignment. It should be slightly more sensitive now. +- Many tiny bug fixes, mostly related to anchored alignment. It should be slightly more sensitive now. - Two overlap modes merged from the dev branch: '-w owler' (fast, uses a trimmed GraphMap pipeline, reports output in the MHAP format) and '-w overlapper' (full GraphMap pipeline including alignment, output in SAM format). For usage - check examples at the bottom. +Owler mode (Overlap With Long Erroneous Reads) skips the graph-mapping and alignments steps. The full pipeline consists of: +1. Construct a gapped spaced index of the reads for only one shape (6-mers, "1111110111111"). +2. For a read, collect all gapped spaced seed hits. +3. LCSk. +4. Filtering seeds reported by LCSk. +5. Output overlaps in MHAP-like format (instead of Jaccard score, fraction of bases covered by seeds is reported; instead of '# shared min-mers' the number of seeds which survived filtering is reported). Other formats will be supported soon. + ### Quick start on Linux x64 ```